@article {pmid39438902,
year = {2024},
author = {Díaz-García, C and Moreno, E and Talavera-Rodríguez, A and Martín-Fernández, L and González-Bodí, S and Martín-Pedraza, L and Pérez-Molina, JA and Dronda, F and Gosalbes, MJ and Luna, L and Vivancos, MJ and Huerta-Cepas, J and Moreno, S and Serrano-Villar, S},
title = {Fecal microbiota transplantation alters the proteomic landscape of inflammation in HIV: identifying bacterial drivers.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {214},
pmid = {39438902},
issn = {2049-2618},
abstract = {BACKGROUND: Despite effective antiretroviral therapy, people with HIV (PWH) experience persistent systemic inflammation and increased morbidity and mortality. Modulating the gut microbiome through fecal microbiota transplantation (FMT) represents a novel therapeutic strategy. We aimed to evaluate proteomic changes in inflammatory pathways following repeated, low-dose FMT versus placebo.<br><br>METHODS: This double-masked, placebo-controlled pilot study assessed the proteomic impacts of weekly FMT versus placebo treatment over 8&#xa0;weeks on systemic inflammation in 29 PWH receiving stable antiretroviral therapy (ART). Three stool donors with high Faecalibacterium and butyrate profiles were selected, and their individual stools were used for FMT capsule preparation. Proteomic changes in 345 inflammatory proteins in plasma were quantified using the proximity extension assay, with samples collected at baseline and at weeks 1, 8, and 24. Concurrently, we characterized shifts in the gut microbiota composition and annotated functions through shotgun metagenomics. We fitted generalized additive models to evaluate the dynamics of protein expression. We selected the most relevant proteins to explore their correlations with microbiome composition and functionality over time using linear mixed models.<br><br>RESULTS: FMT significantly reduced the plasma levels of 45 inflammatory proteins, including established mortality predictors such as IL6 and TNF-&#x3b1;. We found notable reductions persisting up to 16&#xa0;weeks after the final FMT procedure, including in the expression of proteins such as CCL20 and CD22. We identified changes in 46 proteins, including decreases in FT3LG, IL6, IL10RB, IL12B, and IL17A, which correlated with multiple bacterial species. We found that specific bacterial species within the Ruminococcaceae, Succinivibrionaceae, Prevotellaceae families, and the Clostridium genus, in addition to their associated genes and functions, were significantly correlated with changes in inflammatory markers.<br><br>CONCLUSIONS: Targeting the gut microbiome through FMT effectively decreased inflammatory proteins in PWH, with sustained effects. These findings suggest the potential of the microbiome as a therapeutic target to mitigate inflammation-related complications in this population, encouraging further research and development of microbiome-based interventions. Video Abstract.},
}
@article {pmid39438713,
year = {2024},
author = {Gibbons, JA and Worthington, LM and Chiu, EG and Kates, HR and Carter, RR and Nelson, R and Zhang, M and Garrett, TJ and Ho, TTB},
title = {Severe anemia in preterm infants associated with increased bacterial virulence potential and metabolic disequilibrium.},
journal = {Pediatric research},
volume = {},
number = {},
pages = {},
pmid = {39438713},
issn = {1530-0447},
abstract = {BACKGROUND: Anemia in preterm infants is associated with gut dysbiosis and necrotizing enterocolitis. Our study aimed to identify the bacterial functions and metabolites that can explain the underlying mechanisms of anemia associated disease conditions.<br><br>METHODS: We conducted a case control study in preterm infants with cases having a hematocrit &#x2264; 25%. The control infants were matched by birth gestational age and weight. Fecal samples were collected before, at the onset, and after the onset of anemia in cases and with matched postnatal age in controls for metagenomics and metabolomics analyzes.<br><br>RESULTS: 18 anemic and 20 control infants with fecal samples collected at 17 days, 5 weeks, and 7 weeks postnatal age were included. Virulence factor potential, decrease in beta diversity evolution, and larger changes in metabolome were associated with severe anemia. Metabolite abundances of N-acetylneuraminate and butyrobetaine were associated with virulence factor potential. Anemic group had decreased prostaglandin and lactic acid levels.<br><br>CONCLUSION: Fecal omics data showed that severe anemia is associated with a pro-inflammatory gut microbiota with more virulent and less commensal anaerobic bacterial activities. Future studies can examine the link between anemia-associated dysbiosis and clinical outcomes and predict an infant-specific hematocrit threshold that negatively affects clinical outcomes.<br><br>IMPACT: Severe anemia in preterm infants contributes to a pro-inflammatory gut with greater bacterial virulence and less commensal bacterial activities. The multiomics approach using non-invasive fecal biospecimens identified functional and metabolic changes in the gut microbiota and these mechanistic changes are plausible explanations for anemia-associated disease conditions in preterm infants. Our findings identified biological changes of the gut environment in severely anemic preterm infants that can offer guidance for clinical management.},
}
@article {pmid39438539,
year = {2024},
author = {Guo, J and Li, Z and Liu, X and Jin, Y and Sun, Y and Yuan, Z and Zhang, W and Wang, J and Zhang, M},
title = {Response of the gut microbiota to changes in the nutritional status of red deer during winter.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {24961},
pmid = {39438539},
issn = {2045-2322},
support = {2572023AW20//National Key Fundamental Research Funds for the Central Universities, China/ ; 2572020BE02//National Key Fundamental Research Funds for the Central Universities, China/ ; QLKH [2023] 11//the Guizhou Forestry Administration Scientific Research Project/ ; 2023GZJB005//the Reward and Subsidy Fund Project of Guizhou Education University, Ministry of Science and Technology of the People's Republic of China and National Natural Science Foundation of China/ ; 32071512//the National Natural Science Foundation of China, NSFC/ ; 2023YFF1305000//National Key Research and Development Program of China: Migration and diffusion mechanism of wild animals and population control technology/ ; ZKKF2022179//the Opening Research Projects for the Think Tanks of Heilongjiang Provincial Universities/ ; },
mesh = {Animals ; *Deer/microbiology ; *Gastrointestinal Microbiome ; *Seasons ; *Nutritional Status ; Feces/microbiology ; Nitrogen/metabolism/analysis ; Creatinine ; },
abstract = {Unravelling abrupt alterations in the gut microbiota of wild species associated with nutritional stress is imperative but challenging for wildlife conservation. This study assessed the nutritional status of wild red deer during winter on the basis of changes in faecal nitrogen (FN) and urea nitrogen/creatinine (UN: C) levels and identified gut microbes associated with nutritional status via nutritional control experiments and metagenomic sequencing. The FN of wild red deer in winter 2022 was significantly lower than that in winter 2021 (p < 0.05, winter 2021: 1.37 ± 0.16% and winter 2022: 1.26 ± 0.22%), and the UN: C ratio increased (winter 2021: 2.19 ± 1.65 and winter 2022: 3.05 ± 3.50). Similar trends were found in late winter, which indicated greater nutritional pressure in winter (2022) and late winter. Compared with winter 2021, abundances of Ructibacterium and Butyrivibrio significantly increased, and Acetatifactor and Cuneatibacter significantly decreased during winter 2022 (p < 0.05). Compared with early winter, the cell growth and death pathways increased and lipid metabolism and its subpathway of secondary bile acid synthesis (ko00121) significantly decreased during late winter (p < 0.05), which was similar to the changes in malnourished experimental red deer. Abrupt alterations in the gut microbiota should receive increased attention when monitoring the nutritional health of wild ungulates. This study provides new insights and critical implications for the conservation of wild ungulate populations.},
}
@article {pmid39438328,
year = {2024},
author = {Varghese, P and Kumar, K and Sarkar, P and Karmakar, S and Shukla, SP and Kumar, S and Bharti, VS and Paul, T and Kantal, D},
title = {Impact of Triclosan on Bacterial Biodiversity and Sediment Enzymes - A Microcosm Study.},
journal = {Bulletin of environmental contamination and toxicology},
volume = {113},
number = {5},
pages = {59},
pmid = {39438328},
issn = {1432-0800},
support = {DST/TMD-EWO-WTI/2K19/EWFH/2019/214//Department of Science and Technology, Govt. of India/ ; },
mesh = {*Triclosan/toxicity ; *Geologic Sediments/microbiology/chemistry ; *Biodiversity ; *Water Pollutants, Chemical/analysis/toxicity ; *Bacteria/drug effects ; },
abstract = {Triclosan (TCS), a widely used antimicrobial biocide, has raised serious concern among the scientific community in recent years owing to its ubiquitous presence around the globe and toxicity to aquatic organisms. The current study investigated the alterations in bacterial diversity, nutrients, and sediment enzyme activity in TCS-exposed sediment. TCS concentrations of 3 mg/L (T1) and 6 mg/L (T2) were applied in a microcosm setup for 28 days to sediment collected from Versova Creek, Mumbai. Among sediment enzymes, dehydrogenase activity exhibited the greatest degree of variability in 3 mg/L exposed sediment. Nitrite, total nitrogen and urease exhibited higher concentrations in 6 mg/L TCS exposed sediment. The concentration of ammonia was observed to be decreasing in treatments exposed to 6 mg/L TCS. Total heterotrophic bacteria exhibited an increase in count in T1 and a decrease in T2. Metagenomics data showed a higher relative abundance of bacteria in T1 compared to T2 on the 28th day of sampling. Proteobacteria was found to be the most abundant phylum in all samples, and their relative abundance was reduced by 0.14% in T1 and 5.48% in T2. The results confirm the alterations in the composition of sediment bacterial communities and their enzymatic activities due to TCS exposure.},
}
@article {pmid39438078,
year = {2024},
author = {Wei, G and Wu, N and Zhao, K and Yang, S and Wang, L and Liu, Y},
title = {DeepCheck: multitask learning aids in assessing microbial genome quality.},
journal = {Briefings in bioinformatics},
volume = {25},
number = {6},
pages = {},
doi = {10.1093/bib/bbae539},
pmid = {39438078},
issn = {1477-4054},
support = {2023YFD2200104//National Key Research and Development Program of China/ ; 32270664//National Natural Science Foundation of China/ ; },
mesh = {*Metagenome ; *Metagenomics/methods ; *Deep Learning ; Genome, Microbial ; Machine Learning ; Software ; },
abstract = {Metagenomic analyses facilitate the exploration of the microbial world, advancing our understanding of microbial roles in ecological and biological processes. A pivotal aspect of metagenomic analysis involves assessing the quality of metagenome-assembled genomes (MAGs), crucial for accurate biological insights. Current machine learning-based methods often treat completeness and contamination prediction as separate tasks, overlooking their inherent relationship and limiting models' generalization. In this study, we present DeepCheck, a multitasking deep learning framework for simultaneous prediction of MAG completeness and contamination. DeepCheck consistently outperforms existing tools in accuracy across various experimental settings and demonstrates comparable speed while maintaining high predictive accuracy even for new lineages. Additionally, we employ interpretable machine learning techniques to identify specific genes and pathways that drive the model's predictions, enabling independent investigation and assessment of these biological elements for deeper insights.},
}
@article {pmid39437661,
year = {2024},
author = {Sreenivasan, CC and Naveed, A and Uprety, T and Soni, S and Jacob, O and Adam, E and Wang, D and Li, F},
title = {Epidemiological investigation of equine rotavirus B outbreaks in horses in central Kentucky.},
journal = {Veterinary microbiology},
volume = {298},
number = {},
pages = {110278},
doi = {10.1016/j.vetmic.2024.110278},
pmid = {39437661},
issn = {1873-2542},
abstract = {Using metagenomic sequencing we identified equine rotavirus group B (ERVB) of ruminant origin in foal diarrhea outbreaks in the 2021 foaling season. To further investigate ERVB occurrence and determine its environmental stability, we collected mare and foal fecal samples from different farms in Central Kentucky during the 2022 foaling season. The RT-qPCR-based analyses showed that ERVB genome was detected in 16.67 % (42/252) of surveyed mare samples and 26.56 % (34/128) of foal samples. Furthermore, 94.12 % (16/17) of collected soil samples and 100 % (13/13) of water samples obtained from the ERVB-positive farm premises also tested weakly positive. In addition, ERVB genome fragments were detected in 58.33 % (7/12) of indoor samples collected from the equipment/barn/hospital wards during the outbreak period. Finally, the seroprevalence study showed 87 % (113/130) of surveyed horse serum samples were positive for ERVB antibodies. Despite unsuccessful attempts in ERVB cultivation, phylogenetic analyses showed that fecal ERVB strains representing 2022 and 2023 foal diarrhea outbreaks, like 2021 strains, were more closely related to ruminant rotavirus B than other viruses. Further sequence analyses revealed that none of the three viral capsid proteins, the primary targets of virus-neutralizing antibodies, exhibited notable mutations among ERVB strains circulated over the past three years. Our data demonstrated that ERVB was widespread in horses on affected farms with extreme stability in the farm environment. These findings continue to support the need for future surveillance of ERVB in horses and the surrounding environment, and the development of effective countermeasures to protect horses against this new viral disease.},
}
@article {pmid39436938,
year = {2024},
author = {Rocha, U and Kasmanas, JC and Toscan, R and Sanches, DS and Magnusdottir, S and Saraiva, JP},
title = {Simulation of 69 microbial communities indicates sequencing depth and false positives are major drivers of bias in prokaryotic metagenome-assembled genome recovery.},
journal = {PLoS computational biology},
volume = {20},
number = {10},
pages = {e1012530},
doi = {10.1371/journal.pcbi.1012530},
pmid = {39436938},
issn = {1553-7358},
abstract = {We hypothesize that sample species abundance, sequencing depth, and taxonomic relatedness influence the recovery of metagenome-assembled genomes (MAGs). To test this hypothesis, we assessed MAG recovery in three in silico microbial communities composed of 42 species with the same richness but different sample species abundance, sequencing depth, and taxonomic distribution profiles using three different pipelines for MAG recovery. The pipeline developed by Parks and colleagues (8K) generated the highest number of MAGs and the lowest number of true positives per community profile. The pipeline by Karst and colleagues (DT) showed the most accurate results (~ 92%), outperforming the 8K and Multi-Metagenome pipeline (MM) developed by Albertsen and collaborators. Sequencing depth influenced the accurate recovery of genomes when using the 8K and MM, even with contrasting patterns: the MM pipeline recovered more MAGs found in the original communities when employing sequencing depths up to 60 million reads, while the 8K recovered more true positives in communities sequenced above 60 million reads. DT showed the best species recovery from the same genus, even though close-related species have a low recovery rate in all pipelines. Our results highlight that more bins do not translate to the actual community composition and that sequencing depth plays a role in MAG recovery and increased community resolution. Even low MAG recovery error rates can significantly impact biological inferences. Our data indicates that the scientific community should curate their findings from MAG recovery, especially when asserting novel species or metabolic traits.},
}
@article {pmid39436609,
year = {2025},
author = {Singer, F and Kuhring, M and Renard, BY and Muth, T},
title = {Moving Toward Metaproteogenomics: A Computational Perspective on Analyzing Microbial Samples via Proteogenomics.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2859},
number = {},
pages = {297-318},
pmid = {39436609},
issn = {1940-6029},
mesh = {*Proteogenomics/methods ; *Microbiota/genetics ; Computational Biology/methods ; Proteomics/methods ; Software ; Databases, Protein ; Metagenomics/methods ; Algorithms ; Metagenome ; Humans ; High-Throughput Nucleotide Sequencing/methods ; Mass Spectrometry/methods ; Proteome/genetics ; },
abstract = {Microbial sample analysis has received growing attention within the last decade, driven by important findings in microbiome research and promising applications in the biotechnological field. Modern mass spectrometry-based methodology has been established in this context, providing sufficient sensitivity, resolution, dynamic range, and throughput to analyze the so-called metaproteome of complex microbial mixtures from clinical or environmental samples. While proteomic analyses were previously restricted to common model organisms, next-generation sequencing technologies nowadays allow for the rapid and cost-efficient characterization of whole metagenomes of microbial consortia and specific genomes from non-model organisms to which microbes contribute by significant amounts. This proteogenomic approach, meaning the combined application of genomic and proteomic methods, enables researchers to create a protein database that presents a tailored blueprint of the microbial sample under investigation. This contribution provides an overview of the computational challenges and opportunities in proteogenomics and metaproteomics as of January 2018. For practical application, we first showcase an integrative proteogenomic method that circumvents existing reference databases by creating sample-specific transcripts. The underlying algorithm uses a graph network approach that combines RNA-Seq and peptide information. As a second example, we provide a tutorial for a simulation tool that estimates the computational limits of detecting microbial non-model organisms. This method evaluates the potential influence of error-tolerant searches and proteogenomic approaches on databases of interest. Finally, we discuss recommendations for developing future strategies that may help overcome present limitations by combining the strengths of genome- and proteome-based methods and moving toward an integrated metaproteogenomics approach.},
}
@article {pmid39436239,
year = {2024},
author = {Cheng, M and Zhou, H and Zhang, H and Zhang, X and Zhang, S and Bai, H and Zha, Y and Luo, D and Chen, D and Chen, S and Ning, K and Liu, W},
title = {Hidden Links Between Skin Microbiome and Skin Imaging Phenome.},
journal = {Genomics, proteomics &amp; bioinformatics},
volume = {},
number = {},
pages = {},
doi = {10.1093/gpbjnl/qzae040},
pmid = {39436239},
issn = {2210-3244},
abstract = {Despite the skin microbiome has been linked to skin health and diseases, its role in modulating human skin appearance remains understudied. Using a total of 1244 face imaging phenomes and 246 cheek metagenomes, we first established three skin age indices by machine learning including skin phenotype age (SPA), skin microbiota age (SMA), and skin integration age (SIA) as surrogates of phenotypic aging, microbial aging, and their combination, respectively. Moreover, we found that besides aging and gender as intrinsic factors, skin microbiome might also play a role in shaping skin imaging phenotypes (SIPs). Skin taxonomic and functional α diversity was positively linked to melanin, pore, pigment, and ultraviolet spot levels, but negatively linked to sebum, lightening, and porphyrins levels. Furthermore, certain species were correlated with specific SIPs, such as sebum and lightening levels negatively correlated with Corynebacterium matruchotii, Staphylococcus capitis, and Streptococcus sanguinis. Notably, we demonstrated skin microbial potential in predicting SIPs, among which the lightening level presented the least error of 1.8%. Lastly, we provided a reservoir of potential mechanisms through which skin microbiome adjusted the SIPs, including the modulation of pore, wrinkle, and sebum levels by cobalamin and heme synthesis pathways, predominantly driven by Cutibacterium acnes. This pioneering study unveils the paradigm for the hidden links between skin microbiome and skin imaging phenome, providing novel insights into how skin microbiome shapes skin appearance and its healthy aging.},
}
@article {pmid39436062,
year = {2024},
author = {Aguirre, EG and Schwartzman, JA},
title = {Metagenome-assembled genomes of Macrocystis-associated bacteria.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0071524},
doi = {10.1128/mra.00715-24},
pmid = {39436062},
issn = {2576-098X},
abstract = {Microbes are important for the development of kelp, but little is understood about the functions encoded by these microbes. Here, we assembled 1,794 metagenome-associated genomes (MAGs) from bacteria that colonize gametophytes of the giant kelp Macrocystis pyrifera. MAGs were grouped into 149 dereplicated strains. Functional annotation is also presented.},
}
@article {pmid39435818,
year = {2024},
author = {He, L and Yan, YT and Yuan, CY and Lin, QS and Yu, DT},
title = {Characteristics of soil viral communities in Cunninghamia lanceolata plantations with different stand ages.},
journal = {Ying yong sheng tai xue bao = The journal of applied ecology},
volume = {35},
number = {9},
pages = {2543-2551},
doi = {10.13287/j.1001-9332.202409.007},
pmid = {39435818},
issn = {1001-9332},
mesh = {*Soil Microbiology ; *Cunninghamia/growth &amp; development/virology ; Soil/chemistry ; Viruses/classification/isolation &amp; purification/genetics ; China ; Virome ; Phosphorus/analysis ; },
abstract = {We investigated the dynamics of soil viral community in Cunninghamia lanceolata plantations with different stand ages (8, 21, 27, and 40 years old) in a subtropical region. The viral metagenomics and bioinformatics analysis were used to analyze the compositional and functional differences of soil viral communities across different stand ages, and to explore the environmental driving factors. The results showed that tailed phages dominated soil viral community in subtropical C. lanceolata plantations, with the highest proportion of Siphoviridae (19.6%-39.5%). There was significant difference in soil viral community structure among different stand ages, with the main driving factors being electrical conductance and available phosphorus. The metabolic functional genes encoded by viruses exhibited higher relative abundance. The α-diversity of soil viral function in mature C. lanceolata plantations was higher than other stands. There were significant differences in soil viral functional structure among different stand ages, which were mainly driven by ammonium nitrogen. During the development of C. lanceolata plantations, auxiliary metabolic genes encoded by virus related to nitrogen and phosphorus may regulate the metabolism of host microorganisms, thereby potentially impacting biogeochemical cycling of these elements.},
}
@article {pmid39435753,
year = {2024},
author = {Deng, A and Wang, J and Li, L and Shi, R and Li, X and Wen, T},
title = {Synoptic Variation Drives Genetic Diversity and Transmission Mode of Airborne DNA Viruses in Urban Space.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e2404512},
doi = {10.1002/advs.202404512},
pmid = {39435753},
issn = {2198-3844},
support = {XDA17010503//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; CASPMI202202//Open Project Program of CAS Key Laboratory of Pathogenic Microbiology and Immunology/ ; 2024AC010//Central Government Special Fund for Building World-Class Universities (Disciplines) and Guiding Special Development/ ; 2024RC017//Starting Grants Program for Young Talents at China Agricultural University/ ; },
abstract = {Airborne viruses are ubiquitous and play critical roles in maintaining ecosystem balance, however, they remain unexplored. Here, it is aimed to demonstrate that highly diverse airborne viromes carry out specific metabolic functions and use different transmission modes under different air quality conditions. A total of 263.5-Gb data are collected from 13 air samples for viral metagenomic analysis. After assembly and curation, a total of 12 484 viral contigs (1.5-184.2 kb) are assigned to 221 genus-level clades belonging to 47 families, 19 orders, and 15 classes. The composition of viral communities is influenced by weather conditions, with the main biomarker being Caudoviricetes. The most dominant viruses in these air samples belong to the dsDNA Caudoviricetes (54.0%) and ssDNA Repensiviricetes (31.2%) classes. Twelve novel candidate viruses are identified at the order/family/genus levels by alignment of complete genomes and core genes. Notably, Caudoviricetes are highly prevalent in cloudy and smoggy air, whereas Repensiviricetes are highly dominant in sunny and rainy air. Diverse auxiliary metabolic genes of airborne viruses are mainly involved in deoxynucleotide synthesis, implying their unique roles in atmosphere ecosystem. These findings deepen the understanding of the meteorological impacts on viral composition, transmission mode, and ecological roles in the air that we breathe.},
}
@article {pmid39435348,
year = {2024},
author = {Li, Y and Shen, Y and Yang, H and Li, M and Jiang, L and Ma, W and Zhou, F and Su, T},
title = {Q Fever-Related Glomerulonephritis Unveiled by Metagenomic Next-Generation Sequencing.},
journal = {Kidney international reports},
volume = {9},
number = {10},
pages = {3062-3066},
pmid = {39435348},
issn = {2468-0249},
}
@article {pmid39435150,
year = {2024},
author = {Fu, Q and Ma, K and Zhao, J and Li, J and Wang, X and Zhao, M and Fu, X and Huang, D and Chen, H},
title = {Metagenomics unravel distinct taxonomic and functional diversities between terrestrial and aquatic biomes.},
journal = {iScience},
volume = {27},
number = {10},
pages = {111047},
pmid = {39435150},
issn = {2589-0042},
abstract = {Microbes in terrestrial and aquatic ecosystems play crucial roles in driving ecosystem functions, but currently, there is a lack of comparison regarding their taxonomic and functional diversities. Here, we conducted a global analysis to investigate the disparities in microbial taxonomy and microbial-mediated biogeochemical cycles between terrestrial and aquatic ecosystems. Results showed a higher relative abundance of bacteria, especially Actinobacteria and Acidobacteria, in soil than water metagenomes, leading to a greater proportion of genes related to membrane transport, regulatory, and cellular signaling. Moreover, there was a higher abundance of genes associated with carbohydrate, sulfur, and potassium metabolisms in the soil, while those involved in nitrogen and iron metabolisms were more prevalent in the water. Thus, both soil and water microbiomes exhibited unique taxonomic and functional properties associated with biogeochemical processes, providing valuable insights into predicting and understanding the adaptation of microbes in different ecosystems in the face of climate change.},
}
@article {pmid39434927,
year = {2024},
author = {Gong, Y and Wang, T},
title = {Toxoplasmosis-Associated Hemophagocytic Lymphohistiocytosis in a Liver Transplant Recipient.},
journal = {Cureus},
volume = {16},
number = {10},
pages = {e71843},
pmid = {39434927},
issn = {2168-8184},
abstract = {Toxoplasmosis is a rare parasitic infectious disease in solid organ transplant recipients. The disease is characterized by difficulties in diagnosis and high mortality. However, there have been no reported cases of hemophagocytic lymphohistiocytosis (HLH) caused by toxoplasmosis in liver transplant patients. Here, we present the case of an adult female liver transplant recipient who experienced a fatal outcome and developed secondary HLH following confirmation of toxoplasmosis through metagenomic next-generation sequencing. The patient exhibited symptoms, including high fever, skin rash, unconsciousness, and multiorgan failure. The condition met six out of eight criteria for HLH according to the HLH-2004 diagnostic criteria. Additionally, the H-score for this patient was 287 points, confirming the diagnosis of HLH. This represents the first reported case of toxoplasmosis-associated secondary HLH in an adult liver transplant recipient in China.},
}
@article {pmid39434799,
year = {2024},
author = {Ghabban, H and Albalawi, DA and Al-Otaibi, AS and Alshehri, D and Alenzi, AM and Alatawy, M and Alatawi, HA and Alnagar, DK and Bahieldin, A},
title = {Investigating the bacterial community of gray mangroves (Avicennia marina) in coastal areas of Tabuk region.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e18282},
pmid = {39434799},
issn = {2167-8359},
mesh = {*Soil Microbiology ; *Avicennia/microbiology ; Saudi Arabia ; *Bacteria/genetics/classification/isolation &amp; purification ; *Microbiota/genetics ; *RNA, Ribosomal, 16S/genetics ; Rhizosphere ; Wetlands ; },
abstract = {Mangrove vegetation, a threatened and unique inter-tidal ecosystem, harbours a complex and largely unexplored bacterial community crucial for nutrient cycling and the degradation of toxic pollutants in coastal areas. Despite its importance, the bacterial community composition of the gray mangrove (Avicennia marina) in the Red Sea coastal regions remains under-studied. This study aims to elucidate the structural and functional diversity of the microbiome in the bulk and rhizospheric soils associated with A. marina in the coastal areas of Ras Alshabaan-Umluj (Umluj) and Almunibrah-Al-Wajh (Al-Wajh) within the Tabuk region of Saudi Arabia. Amplicon sequencing targeting the 16S rRNA was performed using the metagenomic DNAs from the bulk and rhizospheric soil samples from Umluj and Al-Wajh. A total of 6,876 OTUs were recovered from all samples, of which 1,857 OTUs were common to all locations while the total number of OTUs unique to Al-wajh was higher (3,011 OTUs) than the total number of OTUs observed (1,324 OTUs) at Umluj site. Based on diversity indices, overall bacterial diversity was comparatively higher in rhizospheric soil samples of both sites. Comparing the diversity indices for the rhizosphere samples from the two sites revealed that the diversity was much higher in the rhizosphere samples from Al-Wajh as compared to those from Umluj. The most dominant genera in rhizosphere sample of Al-Wajh were Geminicoccus and Thermodesulfovibrio while the same habitat of the Umluj site was dominated by Propionibacterium, Corynebacterium and Staphylococcus. Bacterial functional potential prediction analyses showed that bacteria from two locations have almost similar patterns of functional genes including amino acids and carbohydrates metabolisms, sulfate reduction and C-1 compound metabolism and xenobiotics biodegradation. However, the rhizosphere samples of both sites harbour more genes involved in the utilization and assimilation of C-1 compounds. Our results reveal that bacterial communities inhabiting the rhizosphere of A. marina differed significantly from those in the bulk soil, suggesting a possible role of A. marina roots in shaping these bacterial communities. Additionally, not only vegetation but also geographical location appears to influence the overall bacterial composition at the two sites.},
}
@article {pmid39434791,
year = {2024},
author = {Zambrano-Alvarado, JI and Uyaguari-Diaz, MI},
title = {Insights into water insecurity in Indigenous communities in Canada: assessing microbial risks and innovative solutions, a multifaceted review.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e18277},
pmid = {39434791},
issn = {2167-8359},
mesh = {Humans ; Canada/epidemiology ; *Drinking Water/microbiology ; *Water Microbiology ; Water Insecurity ; Water Supply ; Water Purification/methods ; Water Quality ; Indigenous Canadians ; },
abstract = {Canada is considered a freshwater-rich country, despite this, several Indigenous reserves struggle with household water insecurity. In fact, some of these communities have lacked access to safe water for almost 30 years. Water quality in Canadian Indigenous reserves is influenced by several factors including source water quality, drinking water treatments applied, water distribution systems, and water storage tanks when piped water is unavailable. The objective of this multifaceted review is to spot the challenges and consequences of inadequate drinking water systems (DWS) and the available technical and microbiological alternatives to address water sanitation coverage in Indigenous reserves of Canada, North America (also known as Turtle Island). A comprehensive literature review was conducted using national web portals from both federal and provincial governments, as well as academic databases to identify the following topics: The status of water insecurity in Indigenous communities across Canada; Microbiological, chemical, and natural causes contributing to water insecurity; Limitations of applying urban-style drinking water systems in Indigenous reserves in Canada and the management of DWS for Indigenous communities in other high-income countries; and the importance of determining the microbiome inhabiting drinking water systems along with the cutting-edge technology available for its analysis. A total of 169 scientific articles matched the inclusion criteria. The major themes discussed include: The status of water insecurity and water advisories in Canada; the risks of pathogenic microorganisms (i.e., Escherichia coli and total coliforms) and other chemicals (i.e., disinfection by-products) found in water storage tanks; the most common technologies available for water treatment including coagulation, high- and low-pressure membrane filtration procedures, ozone, ion exchange, and biological ion exchange and their limitations when applying them in remote Indigenous communities. Furthermore, we reviewed the benefits and drawbacks that high throughput tools such as metagenomics (the study of genomes of microbial communities), culturomics (a high-efficiency culture approach), and microfluidics devices (microminiaturized instruments) and what they could represent for water monitoring in Indigenous reserves. This multifaceted review demonstrates that water insecurity in Canada is a reflection of the institutional structures of marginalization that persist in the country and other parts of Turtle Island. DWS on Indigenous reserves are in urgent need of upgrades. Source water protection, and drinking water monitoring plus a comprehensive design of culturally adapted, and sustainable water services are required. Collaborative efforts between First Nations authorities and federal, provincial, and territorial governments are imperative to ensure equitable access to safe drinking water in Indigenous reserves.},
}
@article {pmid39434181,
year = {2024},
author = {Chen, CZ and Li, P and Liu, L and Sun, YJ and Ju, WM and Li, ZH},
title = {Seasonal variations of microbial communities and viral diversity in fishery-enhanced marine ranching sediments: insights into metabolic potentials and ecological interactions.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {209},
pmid = {39434181},
issn = {2049-2618},
support = {42277269//National Natural Science Foundation of China/ ; 42277269//National Natural Science Foundation of China/ ; 42277269//National Natural Science Foundation of China/ ; 42277269//National Natural Science Foundation of China/ ; KLMR-2022-03//Key Laboratory of Marine Ranching, Ministry of Agriculture and Rural Affairs, China/ ; KLMR-2022-03//Key Laboratory of Marine Ranching, Ministry of Agriculture and Rural Affairs, China/ ; KLMR-2022-03//Key Laboratory of Marine Ranching, Ministry of Agriculture and Rural Affairs, China/ ; KLMR-2022-03//Key Laboratory of Marine Ranching, Ministry of Agriculture and Rural Affairs, China/ ; },
abstract = {BACKGROUND: The ecosystems of marine ranching have enhanced marine biodiversity and ecological balance and have promoted the natural recovery and enhancement of fishery resources. The microbial communities of these ecosystems, including bacteria, fungi, protists, and viruses, are the drivers of biogeochemical cycles. Although seasonal changes in microbial communities are critical for ecosystem functioning, the current understanding of microbial-driven metabolic properties and their viral communities in marine sediments remains limited. Here, we employed amplicon (16S and 18S) and metagenomic approaches aiming to reveal the seasonal patterns of microbial communities, bacterial-eukaryotic interactions, whole metabolic potential, and their coupling mechanisms with carbon (C), nitrogen (N), and sulfur (S) cycling in marine ranching sediments. Additionally, the characterization and diversity of viral communities in different seasons were explored in marine ranching sediments.<br><br>RESULTS: The current study demonstrated that seasonal variations dramatically affected the diversity of microbial communities in marine ranching sediments and the bacterial-eukaryotic interkingdom co-occurrence networks. Metabolic reconstruction of the 113 medium to high-quality metagenome-assembled genomes (MAGs) was conducted, and a total of 8 MAGs involved in key metabolic genes and pathways (methane oxidation&#xa0;-&#xa0;denitrification&#xa0;-&#xa0;S oxidation), suggesting a possible coupling effect between the C, N, and S cycles. In total, 338 viral operational taxonomic units (vOTUs) were identified, all possessing specific ecological characteristics in different seasons and primarily belonging to Caudoviricetes, revealing their widespread distribution and variety in marine sediment ecosystems. In addition, predicted virus-host linkages showed that high host specificity was observed, with few viruses associated with specific hosts.<br><br>CONCLUSIONS: This finding deepens our knowledge of element cycling and viral diversity in fisheries enrichment ecosystems, providing insights into microbial-virus interactions in marine sediments and their effects on biogeochemical cycling. These findings have potential applications in marine ranching management and ecological conservation. Video Abstract.},
}
@article {pmid39434178,
year = {2024},
author = {van Gogh, M and Louwers, JM and Celli, A and Gräve, S and Viveen, MC and Bosch, S and de Boer, NKH and Verheijden, RJ and Suijkerbuijk, KPM and Brand, EC and Top, J and Oldenburg, B and de Zoete, MR},
title = {Next-generation IgA-SEQ allows for high-throughput, anaerobic, and metagenomic assessment of IgA-coated bacteria.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {211},
pmid = {39434178},
issn = {2049-2618},
abstract = {BACKGROUND: The intestinal microbiota plays a significant role in maintaining systemic and intestinal homeostasis, but can also influence diseases such as inflammatory bowel disease (IBD) and cancer. Certain bacterial species within the intestinal tract can chronically activate the immune system, leading to low-grade intestinal inflammation. As a result, plasma cells produce high levels of secretory antigen-specific immunoglobulin A (IgA), which coats the immunostimulatory bacteria. This IgA immune response against intestinal bacteria may be associated with the maintenance of homeostasis and health, as well as disease. Unraveling this dichotomy and identifying the immunostimulatory bacteria is crucial for understanding the relationship between the intestinal microbiota and the immune system, and their role in health and disease. IgA-SEQ technology has successfully identified immunostimulatory, IgA-coated bacteria from fecal material. However, the original technology is time-consuming and has limited downstream applications. In this study, we aimed to develop a next-generation, high-throughput, magnet-based sorting approach (ng-IgA-SEQ) to overcome the limitations of the original IgA-SEQ protocol.<br><br>RESULTS: We show, in various settings of complexity ranging from simple bacterial mixtures to human fecal samples, that our magnetic 96-well plate-based ng-IgA-SEQ protocol is highly efficient at sorting and identifying IgA-coated bacteria in a high-throughput&#xa0;and time efficient&#xa0;manner. Furthermore, we performed a comparative analysis between different IgA-SEQ protocols, highlighting that the original FACS-based IgA-SEQ approach overlooks certain nuances of IgA-coated bacteria, due to the low yield of sorted bacteria. Additionally, magnetic-based ng-IgA-SEQ allows for novel downstream applications. Firstly, as a proof-of-concept, we performed metagenomic shotgun sequencing on 10 human fecal samples to identify IgA-coated bacterial strains and associated pathways and CAZymes. Secondly, we successfully isolated and cultured IgA-coated bacteria by performing the isolation protocol under anaerobic conditions.<br><br>CONCLUSIONS: Our magnetic 96-well plate-based high-throughput next-generation IgA-SEQ technology efficiently identifies a great number of IgA-coated bacteria from fecal samples. This paves the way for analyzing large cohorts as well as novel downstream applications, including shotgun metagenomic sequencing, culturomics, and various functional assays. These downstream applications are essential to unravel the role of immunostimulatory bacteria in health and disease. Video Abstract.},
}
@article {pmid39433961,
year = {2024},
author = {Li, J and Shen, N and He, W and Pan, Y and Wu, J and Zhao, R and Mo, X and Li, Y},
title = {Gut microbiome impact on childhood allergic rhinitis and house dust mite IgE responses.},
journal = {Pediatric research},
volume = {},
number = {},
pages = {},
pmid = {39433961},
issn = {1530-0447},
abstract = {BACKGROUND: The correlation between the gut microbiota and airway inflammation in childhood allergic rhinitis (AR), particularly concerning allergen exposure, remains insufficiently explored. This study aimed to link gut microbiota changes with house dust mite (HDM)-specific IgE responses in pediatric AR.<br><br>METHODS: Using metagenomic shotgun sequencing, we compared the fecal microbiota of 60 children with HDM-AR to 48 healthy controls (HC), analyzing the link to IgE reactions. We examined the effects of oral Escherichia (E.) fergusonii treatment in mice sensitized with ovalbumin and HDM on allergic symptoms, mucosal cell infiltration, Th1/Th2/Tregs balance in the spleen, serum cytokine levels, and E. fergusonii presence in feces.<br><br>RESULTS: Children with HDM-AR have a less diverse gut microbiome and lower levels of E. fergusonii compared to controls, with a negative correlation between E. fergusonii abundance and HDM-specific IgE levels. In mice sensitized with OVA and HDM, oral administration of E. fergusonii improved allergic symptoms, reduced nasal eosinophils/mast cells infiltration and adjusted Th cell populations towards a non-allergic profile in splenic lymphocytes with exception of IFN-&#x3b3; change in serum.<br><br>CONCLUSION: These findings underline the potential of targeting gut microbiota, particularly E. fergusonii, in managing childhood HDM-AR, suggesting a promising approach for future interventions.<br><br>IMPACT: The composition and distribution of gut microbiota in children with HDM-AR are significant changed. The abundance of Escherichia genus is decreased in HDM-AR children. HDM-specific IgE levels are strongly negatively associated with E. fergusonii abundance. Oral administration of E. fergusonii effectively suppresses allergic responses in murine model. These findings offer novel insights into the diagnosis and treatment of HDM-AR, which suggested that E. fergusonii holds promise as a potential therapeutic avenue for managing HDM-AR.},
}
@article {pmid39433727,
year = {2024},
author = {Lemaire, ON and Wegener, G and Wagner, T},
title = {Ethane-oxidising archaea couple CO2 generation to F420 reduction.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {9065},
pmid = {39433727},
issn = {2041-1723},
support = {WA 4053/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; WE 5492/1-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; WA 4053/1-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {*Oxidation-Reduction ; *Carbon Dioxide/metabolism ; *Ethane/metabolism/chemistry ; Archaea/metabolism/genetics ; Aldehyde Oxidoreductases/metabolism/genetics/chemistry ; Multienzyme Complexes/metabolism/genetics/chemistry ; Crystallography, X-Ray ; Archaeal Proteins/metabolism/genetics/chemistry ; Anaerobiosis ; Ferredoxins/metabolism ; Riboflavin/analogs &amp; derivatives ; },
abstract = {The anaerobic oxidation of alkanes is a microbial process that mitigates the flux of hydrocarbon seeps into the oceans. In marine archaea, the process depends on sulphate-reducing bacterial partners to exhaust electrons, and it is generally assumed that the archaeal CO2-forming enzymes (CO dehydrogenase and formylmethanofuran dehydrogenase) are coupled to ferredoxin reduction. Here, we study the molecular basis of the CO2-generating steps of anaerobic ethane oxidation by characterising native enzymes of the thermophile Candidatus Ethanoperedens thermophilum obtained from microbial enrichment. We perform biochemical assays and solve crystal structures of the CO dehydrogenase and formylmethanofuran dehydrogenase complexes, showing that both enzymes deliver electrons to the F420 cofactor. Both multi-metalloenzyme harbour electronic bridges connecting CO and formylmethanofuran oxidation centres to a bound flavin-dependent F420 reductase. Accordingly, both systems exhibit robust coupled F420-reductase activities, which are not detected in the cell extract of related methanogens and anaerobic methane oxidisers. Based on the crystal structures, enzymatic activities, and metagenome mining, we propose a model in which the catabolic oxidising steps would wire electron delivery to F420 in this organism. Via this specific adaptation, the indirect electron transfer from reduced F420 to the sulphate-reducing partner would fuel energy conservation and represent the driving force of ethanotrophy.},
}
@article {pmid39433639,
year = {2024},
author = {Davidson, IM and Nikbakht, E and Haupt, LM and Ashton, KJ and Dunn, PJ},
title = {Methodological approaches in 16S sequencing of female reproductive tract in fertility patients: a review.},
journal = {Journal of assisted reproduction and genetics},
volume = {},
number = {},
pages = {},
pmid = {39433639},
issn = {1573-7330},
abstract = {BACKGROUND: The female genital tract microbiome has become a particular area of interest in improving assisted reproductive technology (ART) outcomes with the emergence of next-generation sequencing (NGS) technology. However, NGS assessment of microbiomes currently lacks uniformity and poses significant challenges for accurate and precise bacterial population representation.<br><br>OBJECTIVE: As multiple NGS platforms and assays have been developed in recent years for microbiome investigation-including the advent of long-read sequencing technologies-this work aimed to identify current trends and practices undertaken in female genital tract microbiome investigations.<br><br>RESULTS: Areas like sample collection and transport, DNA extraction, 16S amplification vs. metagenomics, NGS library preparation, and bioinformatic analysis demonstrated a detrimental lack of uniformity. The lack of uniformity present is a significant limitation characterised by gap discrepancies in generation and interpretation of results. Minimal consistency was observed in primer design, DNA extraction techniques, sample transport, and bioinformatic analyses.<br><br>CONCLUSION: With third-generation sequencing technology highlighted as a promising tool in microbiota-based research via full-length 16S rRNA sequencing, there is a desperate need for future studies to investigate and optimise methodological approaches of the genital tract microbiome to ensure better uniformity of methods and results interpretation to improve clinical impact.},
}
@article {pmid39432998,
year = {2024},
author = {Ma, ZS and Li, L},
title = {Identifications of the potential in-silico biomarkers in lung cancer tissue microbiomes.},
journal = {Computers in biology and medicine},
volume = {183},
number = {},
pages = {109231},
doi = {10.1016/j.compbiomed.2024.109231},
pmid = {39432998},
issn = {1879-0534},
abstract = {It is postulated that the tumor tissue microbiome is one of the enabling characteristics that can either promote or suppress the ability of tumors to acquire certain hallmarks of cancer. This underscores its critical importance in carcinogenesis, cancer progression, and therapy responses. However, characterizing the tumor microbiomes is extremely challenging because of their low biomass and severe difficulties in controlling laboratory-borne contaminants, which is further aggravated by lack of comprehensively effective computational approaches to identify unique or enriched microbial species associated with cancers. Here we take advantage of a recent computational framework by Ma (2024), termed metagenome comparison (MC) framework (MCF), which can detect treatment-specific, unique or enriched OMUs (operational metagenomic unit), or US/ES (unique/enriched species) when adapted for this study. We apply the MCF to reanalyze four lung cancer tissue microbiome datasets, which include samples from Lung Adenocarcinoma (LUAD), Lung Squamous Cell Carcinoma (LUSC), and their adjacent normal tissue (NT) controls. Our analysis is structured around three distinct schemes: Scheme I-separately detecting the US/ES for each of the four lung cancer microbiome datasets; Scheme II-consolidation of the four datasets followed by detection of US/ES in the combined datasets; Scheme III-construction of the union and intersection sets of US/ES derived from the results of the preceding two schemes. The generated lists of US/ES, including enriched microbial phyla, likely hold significant biomedical value for developing diagnostic and prognostic biomarkers for lung cancer risk assessment, improving the efficacy of immunotherapy, and designing novel microbiome-based therapies in lung cancer research.},
}
@article {pmid39432940,
year = {2024},
author = {Aseem, A and Sagar, P and Reddy, NS and Veleri, S},
title = {The antimicrobial resistance profile in poultry of Central and Southern India is evolving with distinct features.},
journal = {Comparative immunology, microbiology and infectious diseases},
volume = {114},
number = {},
pages = {102255},
doi = {10.1016/j.cimid.2024.102255},
pmid = {39432940},
issn = {1878-1667},
abstract = {Antimicrobial resistance (AMR) is fast emerging and is depleting antibiotics repertoire. Poultry is a major source for AMR because focus to enhance its production by modern practices widely uses antibiotics. India and China are major producers of meat and have hotspots of AMR. The Central and Southern India were predicted as emerging hotspots for AMR in poultry but no data available to substantiate it. To this end, we collected chicken feces from poultry farms in these regions and isolated genomic DNA. Further, shotgun whole genome sequencing was performed for metagenomics analysis. For the first time, we report the AMR gene profiles in poultry from Kerala and Telangana. The samples exhibited a higher prevalence of gram-negative and anaerobic species. The high priority pathogens in India were detected, like E.coli, Clostridium perfringens, Klebsiella pneumonia Staphylococcus aureus, Enterococcous faecalis, Pseudomonas aeruginosa, Bacteriodes fragiles. Conspicuously, the Southern India had the highest abundance of AMR genes than the Central India. E.coli was significantly more prevalent in the southernmost zone of India than in other sites. Our data had many common AMR profile features of the European Union (EU) poultry farms but lacked mcr-1, which was a lately emerged AMR gene in E.coli. Our data revealed the extent of AMR gene evolved in the Central and Southern India. It is comparable to the EU data but severity is lesser than in the EU.},
}
@article {pmid39432783,
year = {2024},
author = {Oguro-Igashira, E and Murakami, M and Mori, R and Kuwahara, R and Kihara, T and Kohara, M and Fujiwara, M and Motooka, D and Okuzaki, D and Arase, M and Toyota, H and Peng, S and Ogino, T and Kitabatake, Y and Morii, E and Hirota, S and Ikeuchi, H and Umemoto, E and Kumanogoh, A and Takeda, K},
title = {The pyruvate-GPR31 axis promotes transepithelial dendrite formation in human intestinal dendritic cells.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {44},
pages = {e2318767121},
doi = {10.1073/pnas.2318767121},
pmid = {39432783},
issn = {1091-6490},
support = {JP21H050430//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP21K07895//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP21gm1010004//Japan Agency for Medical Research and Development (AMED)/ ; JPMJSP213//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; J178501002//BD Biosciences (Becton Dickenson Biosciences)/ ; },
mesh = {Humans ; *Receptors, G-Protein-Coupled/metabolism ; *Dendritic Cells/metabolism ; *Pyruvic Acid/metabolism ; Intestinal Mucosa/metabolism/cytology ; Dendrites/metabolism ; Gastrointestinal Microbiome ; Signal Transduction ; Induced Pluripotent Stem Cells/metabolism/cytology ; Organoids/metabolism ; Intestines/cytology ; },
abstract = {The intestinal lumen is rich in gut microbial metabolites that serve as signaling molecules for gut immune cells. G-protein-coupled receptors (GPCRs) sense metabolites and can act as key mediators that translate gut luminal signals into host immune responses. However, the impacts of gut microbe-GPCR interactions on human physiology have not been fully elucidated. Here, we show that GPR31, which is activated by the gut bacterial metabolite pyruvate, is specifically expressed on type 1 conventional dendritic cells (cDC1s) in the lamina propria of the human intestine. Using human induced pluripotent stem cell-derived cDC1s and a monolayer human gut organoid coculture system, we show that cDC1s extend their dendrites toward pyruvate on the luminal side, forming transepithelial dendrites (TED). Accordingly, GPR31 activation via pyruvate enhances the fundamental function of cDC1 by allowing efficient uptake of gut luminal antigens, such as dietary compounds and bacterial particles through TED formation. Our results highlight the role of GPCRs in tuning the human gut immune system according to local metabolic cues.},
}
@article {pmid39432658,
year = {2024},
author = {Liu, B and Dai, W and Wei, J and Sun, S and Chen, W and Deng, Y},
title = {Knowledge framework and emerging trends of invasive pulmonary fungal infection: A bibliometric analysis (2003-2023).},
journal = {Medicine},
volume = {103},
number = {42},
pages = {e40068},
doi = {10.1097/MD.0000000000040068},
pmid = {39432658},
issn = {1536-5964},
mesh = {Humans ; *Bibliometrics ; Invasive Fungal Infections/epidemiology ; Lung Diseases, Fungal/epidemiology/microbiology ; COVID-19/epidemiology ; },
abstract = {The rising number of immunocompromised people has increased concerns about fungal infections as a severe public health issue. Invasive pulmonary fungal infections (IPFIs) are prevalent and often fatal, particularly for those with weakened immune systems. Understanding IPFIs is crucial. The work aims to offer a concise overview of the field's characteristics, main research areas, development paths, and trends. This study searched the Web of Science Core Collection on June 5, 2024, collecting relevant academic works from 2003 to 2023. Analysis was conducted using CiteSpace, VOSviewer, Bibliometrix Package in R, Microsoft Excel 2019, and Scimago Graphica. The study indicated that the USA, the University of Manchester, and Denning DW led in productivity and impact, while the Journal of Fungi topped the list in terms of publication volume and citations. High-frequency terms include "fungal infection," "invasive," "diagnosis," and "epidemiology." Keyword and trend analysis identified "influenza," "COVID-19," "invasive pulmonary aspergillosis," and "metagenomic next-generation sequencing" as emerging research areas. Over the last 2 decades, research on IPFI has surged, with topics becoming more profound. These insights offer key guidance on current trends, gaps, and the trajectory of IPFI studies.},
}
@article {pmid39432094,
year = {2024},
author = {Shafana Farveen, M and Narayanan, R},
title = {Omic-driven strategies to unveil microbiome potential for biodegradation of plastics: a review.},
journal = {Archives of microbiology},
volume = {206},
number = {11},
pages = {441},
pmid = {39432094},
issn = {1432-072X},
mesh = {*Biodegradation, Environmental ; *Plastics/metabolism ; *Microbiota ; Bacteria/metabolism/genetics/classification ; Proteomics ; Genomics ; Microbial Consortia ; },
abstract = {Plastic waste accumulation has lately been identified as the leading and pervasive environmental concern, harming all living beings, natural habitats, and the global market. Given this issue, developing ecologically friendly solutions, such as biodegradation instead of standard disposal, is critical. To effectively address and develop better strategies, it is critical to understand the inter-relationship between microorganisms and plastic, the role of genes and enzymes involved in this process. However, the complex nature of microbial communities and the diverse mechanisms involved in plastic biodegradation have hindered the development of efficient plastic waste degradation strategies. Omics-driven approaches, encompassing genomics, transcriptomics and proteomics have revolutionized our understanding of microbial ecology and biotechnology. Therefore, this review explores the application of omics technologies in plastic degradation studies and discusses the key findings, challenges, and future prospects of omics-based approaches in identifying novel plastic-degrading microorganisms, enzymes, and metabolic pathways. The integration of omics technologies with advanced molecular technologies such as the recombinant DNA technology and synthetic biology would guide in the optimization of microbial consortia and engineering the microbial systems for enhanced plastic biodegradation under various environmental conditions.},
}
@article {pmid39432083,
year = {2024},
author = {Xu, X and Liu, X and Liu, L and Chen, J and Guan, J and Luo, D},
title = {Metagenomic and transcriptomic profiling of the hypoglycemic and hypotriglyceridemic actions of Tremella fuciformis-derived polysaccharides in high-fat-diet- and streptozotocin-treated mice.},
journal = {Food &amp; function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d4fo01870b},
pmid = {39432083},
issn = {2042-650X},
abstract = {Mushroom polysaccharides have great anti-diabetes potential. The fruiting body of Tremella fuciformis is rich in polysaccharides. However, few studies have been performed to date on T. fuciformis-derived polysaccharides (TPs) in terms of anti-diabetes potential. Our previous studies showed that novel TPs with medium molecular weights exhibited the highest anti-skin aging activities among the tested samples in D-galactose-treated mice. In the present study, the effects of these novel TPs, named TP, on high-fat-diet- and streptozotocin-treated mice were assessed, and their potential biological mechanisms were explored by metagenomic and transcriptomic analyses. Oral administration of TP markedly reduced blood glucose and TG levels, alleviated emaciation, improved anti-oxidant capacity, and protected the functions of β-cells at a dose of 100 mg kg[-1] in diabetic mice. Meanwhile, the taxonomic compositions and functional properties of fecal microbiota were altered considerably by TP, as evidenced by partial restoration of the imbalanced gut microbiota and the higher abundances of Bacteroides, Phocaeicola, Bifidobacterium, and Alistipes compared to the model mice, corresponding to the upregulation of four enriched KEGG pathways of microbial communities such as the digestive system, cardiovascular disease, parasitic infectious disease, and cell growth and death. Further transcriptomic analysis of liver tissues identified 35 enriched KEGG pathways associated with metabolism and cellular signaling processes in response to TP. These results demonstrated the biological mechanisms underlying the hypoglycemic and hypotriglyceridemic activities of TP. The findings expanded our understanding of the anti-diabetic mechanisms for mushroom polysaccharides and provided new clues for future studies.},
}
@article {pmid39431871,
year = {2024},
author = {Tuladhar, ET and Chalise, BS and Khadka, B and Tamang, M and Neupane, J and Poudel, S and Droit, L and Mihindukulasuriya, KA and Elong Ngono, A and Basaula, YN and Shresta, S and Wang, D and Manandhar, KD},
title = {Human immunodeficiency virus-1 genome from patient with fever, Nepal.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0076824},
doi = {10.1128/mra.00768-24},
pmid = {39431871},
issn = {2576-098X},
abstract = {A patient with fever presented to the referral infectious disease hospital in Kathmandu, Nepal. Metagenomic sequencing of the patient's serum recovered a near-complete genome of human immunodeficiency virus-1 (HIV-1), distinct from previous HIV-1 genomes from Nepal in GenBank. It shared 92.48% nucleotide identity with an HIV-1 subtype C isolate from India.},
}
@article {pmid39431789,
year = {2024},
author = {Bickerstaff, JRM and Walsh, T and Court, L and Pandey, G and Ireland, K and Cousins, D and Caron, V and Wallenius, T and Slipinski, A and Rane, R and Escalona, HE},
title = {Chromosome structural rearrangements in invasive haplodiploid ambrosia beetles revealed by the genomes of Euwallacea fornicatus (Eichhoff) and Euwallacea similis (Ferrari) (Coleoptera, Curculionidae, Scolytinae).},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evae226},
pmid = {39431789},
issn = {1759-6653},
abstract = {Bark and ambrosia beetles are among the most ecologically and economically damaging introduced plant pests worldwide. Life history traits including polyphagy, haplodiploidy, inbreeding polygyny and symbiosis with fungi contribute to their dispersal and impact. Species vary in their interactions with host trees, with many attacking stressed or recently dead trees, such as the globally distributed E. similis (Ferrari). Other species, like the Polyphagous Shot Hole Borer (PSHB) Euwallacea fornicatus (Eichhoff), can attack over 680 host plants and is causing considerable economic damage in several countries. Despite their notoriety, publicly accessible genomic resources for Euwallacea Hopkins species are scarce, hampering our understanding of their invasive capabilities as well as modern control measures, surveillance and management. Using a combination of long and short read sequencing platforms we assembled and annotated high quality (BUSCO > 98% complete) pseudo-chromosome level genomes for these species. Comparative macro-synteny analysis identified an increased number of pseudo-chromosome scaffolds in the haplodiploid inbreeding species of Euwallacea compared to diploid outbred species, due to fission events. This suggests that life history traits can impact chromosome structure. Further, the genome of E. fornicatus had a higher relative proportion of repetitive elements, up to 17% more, than E. similis. Metagenomic assembly pipelines identified microbiota associated with both species including Fusarium fungal symbionts and a novel Wolbachia strain. These novel genomes of haplodiploid inbreeding species will contribute to the understanding of how life history traits are related to their evolution and to the management of these invasive pests.},
}
@article {pmid39431768,
year = {2024},
author = {Tutagata, J and Pocquet, N and Trouche, B and Reveillaud, J},
title = {Dissection of Mosquito Ovaries, Midgut, and Salivary Glands for Microbiome Analyses at the Organ Level.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {212},
pages = {},
doi = {10.3791/67128},
pmid = {39431768},
issn = {1940-087X},
mesh = {Animals ; Female ; *Salivary Glands/microbiology ; *Microbiota/physiology ; *Ovary/microbiology ; Dissection/methods ; Culicidae/microbiology ; },
abstract = {The global burden of mosquito-transmitted diseases, including malaria, dengue, West Nile, Zika, Usutu, and yellow fever, continues to increase, posing a significant public health threat. With the rise of insecticide resistance and the absence of effective vaccines, new strategies are emerging that focus on the mosquito's microbiota. Nevertheless, the majority of symbionts remain resistant to cultivation. Characterizing the diversity and function of bacterial genomes in mosquito specimens, therefore, relies on metagenomics and subsequent assembly and binning strategies. The obtention and analysis of Metagenome-Assembled Genomes (MAGs) from separated organs can notably provide key information about the specific role of mosquito-associated microbes in the ovaries (the reproductive organs), the midgut (key for food digestion and immunity), or the salivary glands (essential for the transmission of vector-borne diseases as pathogens must colonize them to enter the saliva and reach the bloodstream during a blood meal). These newly reconstructed genomes can then pave the way for the development of novel vector biocontrol strategies. To this aim, it is required to isolate mosquito organs while avoiding cross-contamination between them or with microorganisms present in other mosquito organs. Here, we describe an optimized and contamination-free dissection protocol for studying mosquito microbiome at the organ level.},
}
@article {pmid39431465,
year = {2024},
author = {Hagan, J},
title = {Mapping the spread of antibiotic resistance genes in the coastal microbiome.},
journal = {BioTechniques},
volume = {},
number = {},
pages = {1-4},
doi = {10.1080/07366205.2024.2416379},
pmid = {39431465},
issn = {1940-9818},
abstract = {StandfirstCoastal environments are becoming increasingly exposed to antibiotics through anthropogenic inputs. But how could emerging metagenomic techniques be used to map the spread of antibiotic resistance genes in the coastal microbiome?[Formula: see text].},
}
@article {pmid39431456,
year = {2024},
author = {Batty, CA and Pearson, VK and Olsson-Francis, K and Morgan, G},
title = {Volatile organic compounds (VOCs) in terrestrial extreme environments: implications for life detection beyond Earth.},
journal = {Natural product reports},
volume = {},
number = {},
pages = {},
doi = {10.1039/d4np00037d},
pmid = {39431456},
issn = {1460-4752},
abstract = {Covering: 1961 to 2024Discovering and identifying unique natural products/biosignatures (signatures that can be used as evidence for past or present life) that are abundant, and complex enough that they indicate robust evidence of life is a multifaceted process. One distinct category of biosignatures being explored is organic compounds. A subdivision of these compounds not yet readily investigated are volatile organic compound (VOCs). When assessing these VOCs as a group (volatilome) a fingerprint of all VOCs within an environment allows the complex patterns in metabolic data to be unravelled. As a technique already successfully applied to many biological and ecological fields, this paper explores how analysis of volatilomes in terrestrial extreme environments could be used to enhance processes (such as metabolomics and metagenomics) already utilised in life detection beyond Earth. By overcoming some of the complexities of collecting VOCs in remote field sites, a variety of lab based analytical equipment and techniques can then be utilised. Researching volatilomics in astrobiology requires time to characterise the patterns of VOCs. They must then be differentiated from abiotic (non-living) signals within extreme environments similar to those found on other planetary bodies (analogue sites) or in lab-based simulated environments or microcosms. Such an effort is critical for understanding data returned from past or upcoming missions, but it requires a step change in approach which explores the volatilome as a vital additional tool to current 'Omics techniques.},
}
@article {pmid39431411,
year = {2024},
author = {Sobala, &#x141;F},
title = {LukProt: A database of eukaryotic predicted proteins designed for investigations of animal origins.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evae231},
pmid = {39431411},
issn = {1759-6653},
abstract = {The origins and early evolution of animals is a subject with many outstanding questions. One problem faced by researchers trying to answer them is the absence of a comprehensive database with sequences from non-bilaterians. Publicly available data is plentiful but scattered and often not associated with proper metadata. A new database presented in this paper, LukProt, is an attempt at solving this issue. The database contains protein sequences obtained mostly from genomic, transcriptomic and metagenomic studies and is an extension of EukProt (Richter et al., 2022, Peer Community Journal, 2, e56). LukProt adopts the EukProt naming conventions and includes data from 216 additional animals. The database is associated with a taxonomic grouping (taxogroup) scheme suitable for studying early animal evolution. Minor updates to the database will contain species additions or metadata corrections and major updates will synchronize LukProt to each new version of EukProt and releases are permanently stored on Zenodo (https://doi.org/10.5281/zenodo.7089120). A BLAST server to search the database is available at https://lukprot.hirszfeld.pl/. Users are invited to participate in maintaining and correcting LukProt. As it can be searched without downloading locally, the database can be a convenient resource not only for evolutionary biologists, but for the broader scientific community as well.},
}
@article {pmid39431214,
year = {2024},
author = {Zhu, X and Chen, J and Wu, S and Zeng, J and Sun, Y and Wu, X},
title = {Empyema Caused by Mixed Infection with Streptococcus intermedius and Streptococcus constellatus in a Patient with Previous Surgery for Oral Carcinoma: A Case Report.},
journal = {Infection and drug resistance},
volume = {17},
number = {},
pages = {4447-4454},
pmid = {39431214},
issn = {1178-6973},
abstract = {BACKGROUND: The incidence of community-acquired empyema caused by the Streptococcus anginosus group (SAG) has been on the rise in the 2020s. To the best of our knowledge, while empyema caused individually by either strain has been reported, there are no reports on empyema caused by concurrent infection with these two strains. Here, we report for the first time empyema caused by concurrent infection with Streptococcus intermedius and Streptococcus constellatus (both SAG species) in a postoperative patient who had been treated for floor of the mouth carcinoma.<br><br>CASE PRESENTATION: A 61-year-old male patient who had undergone surgical treatment for floor of the mouth carcinoma 2 year earlier suddenly presented with left-sided chest pain. Chest computed tomography (CT) revealed encapsulated pleural effusion on the left side, which was diagnosed as empyema. Metagenomic next-generation sequencing(mNGS) of the pleural fluid sample indicated mixed infection caused by Streptococcus intermedius and Streptococcus constellatus. The patient's condition improved about 5&#xa0;weeks after treatment with thoracic fluid drainage and cephalosporin antibiotics.<br><br>CONCLUSION: This case highlights the possibility of concurrent infection with two SAG strains in patients with empyema. Currently, it is unclear whether there is a definitive relationship between a surgical history of carcinoma of the floor of the mouth and empyema caused by infection with SAG strains. This case could, perhaps, serve as a reference for future related research on the topic.},
}
@article {pmid39431056,
year = {2024},
author = {Han, L and Hu, C and Du, Z and Yu, H and Du, Y and Li, L and Li, F and Wang, Y and Gao, X and Sun, X and Zhang, Z and Qin, Y},
title = {Association of glycerolipid metabolism with gut microbiota disturbances in a hamster model of high-fat diet-induced hyperlipidemia.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1439744},
pmid = {39431056},
issn = {2235-2988},
mesh = {Animals ; *Hyperlipidemias/metabolism/microbiology ; *Gastrointestinal Microbiome ; *Diet, High-Fat/adverse effects ; Cricetinae ; *Disease Models, Animal ; *Liver/metabolism ; Male ; *Lipid Metabolism ; *Feces/microbiology ; Metabolomics ; Bacteria/classification/isolation &amp; purification/metabolism/genetics ; Metagenomics ; Lipids/blood ; },
abstract = {BACKGROUND: High-fat diet (HFD)-induced hyperlipidemia, which is associated with gut microbiota disturbances, remains a major public health challenge. Glycerolipid metabolism is responsible for lipid synthesis and is thus involved in the development of hyperlipidemia. However, possible association between the HFD-modulated gut microbiome and the glycerolipid metabolism pathway remains unclear.<br><br>METHODS: Hamsters were fed a HFD for 4 weeks to establish a hyperlipidemia model. Fecal, plasma and liver samples collected from hamsters fed a HFD or a normal chow diet (NCD) were used for integrative metagenomic and untargeted metabolomic analyses to explore changes in the composition and functions of the gut microbiota, and relevant metabolites. Spearman rank correlation analysis was used to explore correlations between gut microbes and circulating glycerolipid metabolites, gut microbes and lipids, and circulating glycerolipid metabolites and lipids.<br><br>RESULTS: The gut microbial composition of HFD hamsters showed significant alterations at the phylum, genus, and species levels that were skewed toward metabolic disorders compared with that of NCD hamsters. Functional characterization by KEGG analysis identified enrichment of the glycerolipid metabolism pathway in the gut microbiome of HFD hamsters. Plasma and liver metabolomics further indicated the upregulation and enrichment of glycerolipid metabolites in HFD hamsters. The Faecalibaculum, Allobaculum, and Eubacterium genera were positively correlated with plasma glycerolipid metabolites and lipid indices.<br><br>CONCLUSION: The findings of this study suggest an association between glycerolipid metabolism and the HFD-modulated gut microbiome that is involved in the development of hyperlipidemia.},
}
@article {pmid39430957,
year = {2024},
author = {Yao, QH and Xia, XJ and Zhi, HL and Liu, ZH},
title = {Extensive erythematous plaques of fungal origin in an overseas student: Cutaneous manifestation of coccidioidomycosis.},
journal = {Medical mycology case reports},
volume = {46},
number = {},
pages = {100674},
pmid = {39430957},
issn = {2211-7539},
abstract = {We present a case of Coccidioides posadasii infection which was contracted during study abroad. This coccidioidomycosis showed atypical manifestations and was diagnosed by a combination of tissue biopsy, metagenomic next-generation sequencing, internal transcribed spacer sequencing and culture. Initial treatment with fluconazole was not effective. Antifungal therapy was switched to voriconazole based on drug sensitivity results with good result. This case demonstrates the clinical significance of combining multiple diagnostic methods.},
}
@article {pmid39430728,
year = {2025},
author = {Zhang, Y and Xue, B and Mao, Y and Chen, X and Yan, W and Wang, Y and Wang, Y and Liu, L and Yu, J and Zhang, X and Chao, S and Topp, E and Zheng, W and Zhang, T},
title = {High-throughput single-cell sequencing of activated sludge microbiome.},
journal = {Environmental science and ecotechnology},
volume = {23},
number = {},
pages = {100493},
pmid = {39430728},
issn = {2666-4984},
abstract = {Wastewater treatment plants (WWTPs) represent one of biotechnology's largest and most critical applications, playing a pivotal role in environmental protection and public health. In WWTPs, activated sludge (AS) plays a major role in removing contaminants and pathogens from wastewater. While metagenomics has advanced our understanding of microbial communities, it still faces challenges in revealing the genomic heterogeneity of cells, uncovering the microbial dark matter, and establishing precise links between genetic elements and their host cells as a bulk method. These issues could be largely resolved by single-cell sequencing, which can offer unprecedented resolution to show the unique genetic information. Here we show the high-throughput single-cell sequencing to the AS microbiome. The single-amplified genomes (SAGs) of 15,110 individual cells were clustered into 2,454 SAG bins. We find that 27.5% of the genomes in the AS microbial community represent potential novel species, highlighting the presence of microbial dark matter. Furthermore, we identified 1,137 antibiotic resistance genes (ARGs), 10,450 plasmid fragments, and 1,343 phage contigs, with shared plasmid and phage groups broadly distributed among hosts, indicating a high frequency of horizontal gene transfer (HGT) within the AS microbiome. Complementary analysis using 1,529 metagenome-assembled genomes from the AS samples allowed for the taxonomic classification of 98 SAG bins, which were previously unclassified. Our study establishes the feasibility of single-cell sequencing in characterizing the AS microbiome, providing novel insights into its ecological dynamics, and deepening our understanding of HGT processes, particularly those involving ARGs. Additionally, this valuable tool could monitor the distribution, spread, and pathogenic hosts of ARGs both within AS environments and between AS and other environments, which will ultimately contribute to developing a health risk evaluation system for diverse environments within a One Health framework.},
}
@article {pmid39430384,
year = {2024},
author = {Takahashi, Y and Niwa, H and Ebisuda, Y and Mukai, K and Yoshida, T and Raidal, S and Padalino, B and Ohmura, H},
title = {Increased freedom of head movement mitigates stress and bacterial load in the airways of horses during transport.},
journal = {Frontiers in veterinary science},
volume = {11},
number = {},
pages = {1477653},
pmid = {39430384},
issn = {2297-1769},
abstract = {INTRODUCTION: Protection of horse welfare during transport is crucial. The aim of this study was to determine the effect of head and neck restraint on behavior and airway bacteria.<br><br>METHODS: In a randomized crossover study, six healthy Thoroughbreds were transported by road for 22&#x2009;h in an individual bay with tight head restraint (50&#x2009;cm short-rope) or loose head restraint (95&#x2009;cm long-rope). Behavioral parameters relating to head position, eating, and stress were monitored during transportation. Tracheal wash samples were obtained 6&#x2009;days before and immediately after transport for bacterial culture and metagenomic analysis.<br><br>RESULTS AND DISCUSSION: Compared to before transport, bacterial load (CFU/mL) after transport was significantly increased in the short-rope group (p&#x2009;=&#x2009;0.04), whereas no changes were observed in the long-rope group. Transport significantly reduced Simpson index at phylum, class, order, and family levels in both groups (p <&#x2009;0.001) of tracheal microbiota. In both groups, this reduction was associated with increases in the dominant members of relative abundance at phylum (Firmicutes: +24% in long-rope and +14% in short-rope), class (Bacilli: +20% in long-rope and +22% in short-rope) and family (Streptococcaceae: +22% in long-rope and +23% in short-rope) levels. Licking behavior during transportation with short-rope restraint was more frequent than in horses with long-rope restraint. These results suggest loose head restraint during transportation is likely to ameliorate stress and mitigate the associated increased bacterial load in the lower airways associated with transport. Further, head position during transportation is likely a more important determinant of airway hygiene and distress than duration of travel.},
}
@article {pmid39429886,
year = {2024},
author = {Peng, X and Feng, K and Yang, X and He, Q and Zhao, B and Li, T and Wang, S and Deng, Y},
title = {iNAP 2.0: Harnessing metabolic complementarity in microbial network analysis.},
journal = {iMeta},
volume = {3},
number = {5},
pages = {e235},
pmid = {39429886},
issn = {2770-596X},
abstract = {With the widespread adoption of metagenomic sequencing, new perspectives have emerged for studying microbial ecological networks, yielding metabolic evidence of interspecies interactions that traditional co-occurrence networks cannot infer. This protocol introduces the integrated Network Analysis Pipeline 2.0 (iNAP 2.0), which features an innovative metabolic complementarity network for microbial studies from metagenomics sequencing data. iNAP 2.0 sets up a four-module process for metabolic interaction analysis, namely: (I) Prepare genome-scale metabolic models; (II) Infer pairwise interactions of genome-scale metabolic models; (III) Construct metabolic interaction networks; and (IV) Analyze metabolic interaction networks. Starting from metagenome-assembled or complete genomes, iNAP 2.0 offers a variety of methods to quantify the potential and trends of metabolic complementarity between models, including the PhyloMint pipeline based on phylogenetic distance-adjusted metabolic complementarity, the SMETANA (species metabolic interaction analysis) approach based on cross-feeding substrate exchange prediction, and metabolic distance calculation based on parsimonious flux balance analysis (pFBA). Notably, iNAP 2.0 integrates the random matrix theory (RMT) approach to find the suitable threshold for metabolic interaction network construction. Finally, the metabolic interaction networks can proceed to analysis using topological feature analysis such as hub node determination. In addition, a key feature of iNAP 2.0 is the identification of potentially transferable metabolites between species, presented as intermediate nodes that connect microbial nodes in the metabolic complementarity network. To illustrate these new features, we use a set of metagenome-assembled genomes as an example to comprehensively document the usage of the tools. iNAP 2.0 is available at https://inap.denglab.org.cn for all users to register and use for free.},
}
@article {pmid39429879,
year = {2024},
author = {Lu, YX and Yang, JB and Li, CY and Tian, YH and Chang, RR and Kong, DS and Yang, SL and Wang, YF and Zhang, YB and Zhu, XS and Pan, WH and Kong, SY},
title = {Efficient and easy-to-use capturing three-dimensional metagenome interactions with GutHi-C.},
journal = {iMeta},
volume = {3},
number = {5},
pages = {e227},
pmid = {39429879},
issn = {2770-596X},
abstract = {Hi-C can obtain three-dimensional chromatin structure information and is widely used for genome assembly. We constructed the GutHi-C technology. As shown in the graphical abstract, it is a highly efficient and quick-to-operate method and can be widely used for human, livestock, and poultry gut microorganisms. It provides a reference for the Hi-C methodology of the microbial metagenome. DPBS, Dulbecco's phosphate-buffered saline; Hi-C, high-through chromatin conformation capture; LB, Luria-Bertani; NGS, next-generation sequencing; PCR, polymerase chain reaction; QC, quality control.},
}
@article {pmid39429745,
year = {2024},
author = {Fazal, BZ and Yahya, NA and Ling, CMWV and Wei, YC and Leow, TC and Halim, MA and Balakrishnan, KN and Budiman, C and Amin, Z},
title = {16S rRNA metagenomics data on the bacterial communities in Poring Hot Spring, Sabah, Malaysia.},
journal = {Data in brief},
volume = {57},
number = {},
pages = {110935},
pmid = {39429745},
issn = {2352-3409},
abstract = {Hot springs are known to harbor potentially unique microorganisms due to the extreme temperatures in which they thrive and their biotechnologically important enzymes that are active at high temperature, which are beneficial for various industries. Sabah, Malaysia, houses several hot springs, yet knowledge of their microbiological diversity remains limited. Here, the raw sequence data of bacterial communities in a hot spring through metagenomic analysis are revealed. The data were obtained by collecting water and sediment samples from Poring Hot Spring (PHS) in Ranau, Sabah, and their bacterial diversity was analyzed using 16S rRNA amplicon sequencing targeting the V3-V4 regions. The analysis identified bacterial diversity in both water and sediment samples, with 35 phyla, 76 families, and 90 genera in water, and 38 phyla, 114 families, and 128 genera in sediment. Proteobacteria dominated the water samples (87 %), while Cyanobacteria were most abundant in sediment samples (51 %). The most abundant genera in water were Tepidimonas, Hydrogenophilus and Methylothermus, whereas Geitlerinema, Calothrix and Nitrospira dominated the sediment. Sediment samples exhibited higher bacterial richness and diversity compared to water samples, as indicated by α-diversity analysis. Sequences and sample data are deposited in the NCBI Sequence Read Archive under Bioproject ID PRJNA982554 (Accession number: SRX20671661 to SRX20671666) at https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA982554&amp;o=acc_s%3Aa).},
}
@article {pmid39429648,
year = {2024},
author = {Li, Z and Xu, B and Liu, J},
title = {Acute fibrinous and organizing pneumonia associated with Candida: A case report.},
journal = {Respiratory medicine case reports},
volume = {52},
number = {},
pages = {102120},
pmid = {39429648},
issn = {2213-0071},
abstract = {BACKGROUND: Acute fibrinous and organizing pneumonia (AFOP) is a rare form of pneumonia, is characterized by the deposition of fibrin in alveoli, the formation of fibrin spheres, and deposition of fibrin in alveolar junctions and bronchioles adjacent to or adjacent to the alveoli, forming institutional loose connective tissue.The clinical characteristics of AFOP lack specificity. We report a special case of AFOP that may be associated with Candida, so as to improve our understanding and diagnosis of AFOP.<br><br>RESULT: In this patient who was early misdiagnosed with community-acquired pneumonia (CAP), the empirical anti-infective treatment was ineffective, and various infectious and non-infectious factors were excluded. Flexible bronchoscopy was subsequently performed, and metagenomics Next Generation Sequencing (mNGS) of Bronchoalveolar lavage fluid (BALF) showed Candida albicans, and further ultrasound interventional percutaneous and lung puncture biopsy was performed to diagnose AFOP according to pathology, while mNGS of lung pathological tissue also suggested Candid. The patient recovered well on corticosteroids.<br><br>CONCLUSION: The clinical manifestation, laboratory examination and imaging examination of AFOP has no specificity, lung biopsy and pathological examination should be carried out to make a clear diagnosis by comprehensively considering the clinical manifestations, auxiliary examination, pathology and other aspects of the patients. After definite diagnosis, it is still necessary to rule out various diseases and environmental exposure and further classify them as idiopathic or secondary, so as to choose monotherapy or combination therapy.},
}
@article {pmid39428758,
year = {2024},
author = {Minot, SS and Mayer-Blackwell, K and Fiore-Gartland, A and Johnson, A and Self, S and Bhatti, P and Yao, L and Liu, L and Sun, X and Jinfa, Y and Kublin, J},
title = {Species- and subspecies-level characterization of health-associated bacterial consortia that colonize the human gut during infancy.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2414975},
doi = {10.1080/19490976.2024.2414975},
pmid = {39428758},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; Infant ; *Feces/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Male ; Female ; Metagenomics ; Microbial Consortia ; Metagenome ; Infant, Newborn ; Cohort Studies ; Cystic Fibrosis/microbiology ; },
abstract = {BACKGROUND: The human gut microbiome develops rapidly during infancy, a key window of development coinciding with the maturation of the adaptive immune system. However, little is known about the microbiome growth dynamics over the first few months of life and whether there are any generalizable patterns across human populations. We performed metagenomic sequencing on stool samples (n = 94) from a cohort of infants (n = 15) at monthly intervals in the first 6 months of life, augmenting our dataset with seven published studies for a total of 4,441 metagenomes from 1,162 infants.<br><br>RESULTS: Strain-level de novo analysis was used to identify 592 of the most abundant organisms in the infant gut microbiome. Previously unrecognized consortia were identified which exhibited highly correlated abundances across samples and were composed of diverse species spanning multiple genera. Analysis of a published cohort of infants with cystic fibrosis identified one such novel consortium of diverse Enterobacterales which was positively correlated with weight gain. While all studies showed an increased community stability during the first year of life, microbial dynamics varied widely in the first few months of life, both by study and by individual.<br><br>CONCLUSION: By augmenting published metagenomic datasets with data from a newly established cohort, we were able to identify novel groups of organisms that are correlated with measures of robust human development. We hypothesize that the presence of these groups may impact human health in aggregate in ways that individual species may not in isolation.},
}
@article {pmid39428055,
year = {2024},
author = {Hazra, D and Chawla, K and Fayaz, SM and Sintchenko, V and Magazine, R and Martinez, E and Pandey, A},
title = {The impact of anti-tuberculosis treatment on respiratory tract microbiome in pulmonary tuberculosis.},
journal = {Microbes and infection},
volume = {},
number = {},
pages = {105432},
doi = {10.1016/j.micinf.2024.105432},
pmid = {39428055},
issn = {1769-714X},
abstract = {The growing evidence has underscored the significance of interactions between the host and microbiota in respiratory health, presenting a novel perspective on disease management. Yet, comprehension of the respiratory microbiome shifts before and after anti-tuberculosis treatment is limited. This study compares respiratory microbiome profiles in untreated tuberculosis (UTB) and completed TB treatment (CTB) cases with healthy controls, using 16S rRNA sequencing on sputum samples. Significant reduction in sputum microbial alpha diversity was observed in both TB groups when compared to healthy controls (P<0.05). Beta diversity analysis showed distinct clustering (P<0.05). Linear discriminant analysis revealed an abundance of potentially pathogenic bacterial genera like Haemophilus, Pseudomonas, and Mycobacterium in the UTB group, while Streptococcus, Rothia, and Neisseria dominated in CTB samples. Healthy sputum microbiomes were enriched with Prevotella, Fusobacterium, Porphyromonadaceae_unclassified, Peptostreptococcus. Moreover, predicted bacterial functional pathways showed significant differences among the three groups, mainly related to nutrient metabolism. These findings indicated significant microbial dysbiosis in sputum samples recovered from patients with pulmonary TB with an elevated presence of potentially pathogenic bacteria, depletion of beneficial genera, and downregulation of several essential metabolic pathways. Further exploration of respiratory microbiome-based diagnostic biomarkers and their role in targeted treatment strategies in tuberculosis is warranted.},
}
@article {pmid39427901,
year = {2024},
author = {Shruti, VC and Kutralam-Muniasamy, G and Pérez-Guevara, F},
title = {Viruses in the era of microplastics and plastispheres: Analytical methods, advances and future directions.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {177010},
doi = {10.1016/j.scitotenv.2024.177010},
pmid = {39427901},
issn = {1879-1026},
abstract = {Research on microplastics and plastispheres now incorporates the study of viruses to evaluate their effects on the environment and human health. Sharing these new discoveries with the scientific community is crucial to fostering further research and collaborations. However, the current research and methodologies used are fragmented. To address this issue, this paper reviews the literature and the use of methodology developments in each study, identifying four emerging research areas: (1) viral interactions with microplastics; (2) viral population, diversity, and function in plastispheres; (3) the effects of viruses and plastic particles in host-associated environments; and (4) the impacts of viruses within plastispheres. To that end, the article is structured to streamline navigation and help readers easily access existing approaches, recent advancements, key findings, challenges, and opportunities in these areas. Our synthesis reveals that research methods include biochemical assays, omics techniques, spectroscopic analysis, and molecular and bioinformatic tools. Various mechanisms enable viruses to attach to microplastics and plastispheres, leading to widespread distribution and contributing to toxic effects and gene transfer. While the growing evidence is intriguing, there is still much to uncover about their ecological interactions, functions, and impacts.},
}
@article {pmid39427542,
year = {2024},
author = {Kuai, Y and Yao, Z and Pang, T and Wang, L and Gong, X and Cheng, Y and Liu, X and Fu, Q and Wang, S},
title = {Chronic dietary deoxynivalenol exposure interferes the intestinal microbial community structure and antibiotic resistome in laying hens.},
journal = {Ecotoxicology and environmental safety},
volume = {286},
number = {},
pages = {117213},
doi = {10.1016/j.ecoenv.2024.117213},
pmid = {39427542},
issn = {1090-2414},
abstract = {Antibiotic resistance genes (ARGs) are critical emerging pollutants that have attracted considerable attention. Deoxynivalenol (DON) is one of the most prevalent mycotoxins in cereal crops worldwide, arising severe health hazards to both humans and animals. Even if numerous researches argue in favor of a notorious influence of DON on the gut, the effects of dietary DON exposure on the ARG profile in poultry intestine remain obscure. In this study, two separate feeding experiments using Jing Tint 6 laying hens exposed to 4.5 or 9.0 mg/kg DON were performed to explore the impact of dietary DON exposure on the microbial community structure and the profiles of ARGs in the intestine via 16S rDNA sequencing and metagenomics sequencing, respectively. In addition, growth performance and intestinal barrier function were also determined to assess the feasibility of using DON-contaminated feedstuffs inappropriate for pigs' consumption in laying hens. Chronic ingestion of DON at 9.0 mg/kg did not alter zootechnical parameters. However, histomorphological impairments were observed in liver and jejunum. Additionally, metagenomic sequencing revealed that dietary DON exposure at 9.0 mg/kg level dramatically changed the gut microbial structure and shifted the ARG profile. The abundance of tetracycline ARG subtype in the layer cecum was decreased, whereas the abundance of vancomycin ARG subtype was increased upon DON exposure. Co-occurrence network analysis identified that Prevotella was the major ARG host in the intestine of laying hens. In summary, our findings demonstrated that DON-contaminated feedstuffs inappropriate for pigs' consumption should be prudently used in hen production, and shed new light on the interactions between mycotoxins and ARGs in the poultry intestine.},
}
@article {pmid39427349,
year = {2024},
author = {Zhou, L and Zhang, X and Zhang, X and Wu, P and Wang, A},
title = {Insights into the carbon and nitrogen metabolism pathways in mixed-autotrophy/heterotrophy anammox consortia in response to temperature reduction.},
journal = {Water research},
volume = {268},
number = {Pt A},
pages = {122642},
doi = {10.1016/j.watres.2024.122642},
pmid = {39427349},
issn = {1879-2448},
abstract = {While the multi-coupled anammox system boasts a substantial research foundation, the specific characteristics of its synergistic metabolic response to decreased temperatures, particularly within the range of 13-15 °C, remained elusive. In this study, we delve into the intricate carbon and nitrogen metabolism pathways of mixed-autotrophy/heterotrophy anammox consortia under conditions of temperature reduction. Our macrogenomic analyses reveal a compelling phenomenon: the stimulation of functional genes responsible for complete denitrification, suggesting an enhancement of this process during temperature reduction. This adaptation likely contributes to maintaining system performance amidst environmental challenges. Further metabolic functional recombination analyses highlight a dramatic shift in microbial community composition, with denitrifying MAGs (metagenome-assembled genomes) experiencing a substantial increase in abundance (up to 200 times) compared to autotrophic MAGs. This proliferation underscores the strong stimulatory effect of temperature reduction on denitrifying species. Notably, autotrophic MAGs play a pivotal role in supporting the glycolytic processes of denitrifying MAGs, underscoring the intricate interdependencies within the consortia. Moreover, metabolic variations in amino acid composition among core MAGs emerge as a crucial adaptation mechanism. These differences facilitate the preservation of enzyme activity and enhance the consortia's resilience to low temperatures. Together, these findings offer a comprehensive understanding of the microbial synergistic metabolism within mixed-autotrophy/heterotrophy anammox consortia under temperature reduction, shedding light on their metabolic flexibility and resilience in dynamic environments.},
}
@article {pmid39427267,
year = {2024},
author = {Singh, AB and Paul, T and Shukla, SP and Kumar, S and Kumar, S and Kumar, G and Kumar, K},
title = {Gut microbiome as biomarker for triclosan toxicity in Labeo rohita: bioconcentration, immunotoxicity and metagenomic profiling.},
journal = {Ecotoxicology (London, England)},
volume = {},
number = {},
pages = {},
pmid = {39427267},
issn = {1573-3017},
support = {DST/TMD-EWO-WTI/2K19/EWFH/2019/214//Department of Science and Technology, Ministry of Science and Technology, India/ ; },
abstract = {Triclosan (TCS) is a lipophilic, broad spectrum antimicrobial agent commonly used in personal care products with a projected continuous escalation in aquatic environments in the post COVID 19 era. There is rich documentation in the literature on the alteration of physiological responses in fish due to TCS exposure; however, studies on gut associated bacteria of fish are still scarce. This is the first attempt to determine changes in bacterial community structure due to exposure of TCS on Labeo rohita, a commercially essential freshwater species, using 16S V3-V4 region ribosomal RNA (rRNA) next-generation sequencing (NGS). Chronic exposure of TCS at environmentally realistic concentrations viz. 1/5th (T1: 0.129 mg/L) and 1/10th (T2: 0.065 mg/L) of LC50 for 28 days resulted in the dose dependent bioconcentration of TCS in the fish gut. Prolonged exposure to TCS leads to disruption of gut bacteria evidenced by down regulation of the host immune system. Additionally, high-throughput sequencing analysis showed alternation in the abundance and diversity of microbial communities in the gut, signifying Proteobacteria and Verrucomicrobia as dominant phyla. Significant changes were also observed in the relative abundance of Chloroflexi and Gammatimonadetes phyla in TCS exposed groups. The study revealed that gut microbiome can be used as a biomarker in assessing the degree of TCS toxicity in commercially important fish species.},
}
@article {pmid39386691,
year = {2024},
author = {Gustafson, KL and Rodriguez, TR and McAdams, ZL and Coghill, LM and Ericsson, AC and Franklin, CL},
title = {Failure of colonization following gut microbiota transfer exacerbates DSS-induced colitis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39386691},
issn = {2692-8205},
support = {T32 GM008396/GM/NIGMS NIH HHS/United States ; T32 OD011126/OD/NIH HHS/United States ; U42 OD010918/OD/NIH HHS/United States ; },
abstract = {To study the impact of differing specific pathogen-free gut microbiomes (GMs) on a murine model of inflammatory bowel disease, selected GMs were transferred using embryo transfer (ET), cross-fostering (CF), and co-housing (CH). Prior work showed that the GM transfer method and the microbial composition of donor and recipient GMs can influence microbial colonization and disease phenotypes in dextran sodium sulfate-induced colitis. When a low richness GM was transferred to a recipient with a high richness GM via CH, the donor GM failed to successfully colonize, and a more severe disease phenotype resulted when compared to ET or CF, where colonization was successful. By comparing CH and gastric gavage for fecal material transfer, we isolated the microbial component of this effect and determined that differences in disease severity and survival were associated with microbial factors rather than the transfer method itself. Mice receiving a low richness GM via CH and gastric gavage exhibited greater disease severity and higher expression of pro-inflammatory immune mediators compared to those receiving a high richness GM. This study provides valuable insights into the role of GM composition and colonization in disease modulation.},
}
@article {pmid39426981,
year = {2024},
author = {Lu, C and Liu, D and Wu, Q and Zeng, J and Xiong, Y and Luo, T},
title = {EphA2 blockage ALW-II-41-27 alleviates atherosclerosis by remodeling gut microbiota to regulate bile acid metabolism.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {108},
pmid = {39426981},
issn = {2055-5008},
support = {2023NSFSC1631//Department of Science and Technology of Sichuan Province (Sichuan Provincial Department of Science and Technology)/ ; 2023YFS0116//Department of Science and Technology of Sichuan Province (Sichuan Provincial Department of Science and Technology)/ ; 2022YFS0604//Department of Science and Technology of Sichuan Province (Sichuan Provincial Department of Science and Technology)/ ; Q22066//Education Department of Sichuan Province/ ; },
mesh = {Animals ; *Atherosclerosis/metabolism/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Bile Acids and Salts/metabolism ; Mice ; *Receptor, EphA2/metabolism ; *Diet, High-Fat/adverse effects ; Male ; Humans ; Disease Models, Animal ; Plaque, Atherosclerotic/etiology ; Mice, Inbred C57BL ; Bacteria/classification/isolation &amp; purification/genetics/metabolism ; Dysbiosis ; },
abstract = {Coronary artery disease (CAD), a critical condition resulting from systemic inflammation, metabolic dysfunction, and gut microbiota dysbiosis, poses a global public health challenge. ALW-II-41-27, a specific inhibitor of the EphA2 receptor, has shown anti-inflammatory prosperities. However, the impact of ALW-II-41-27 on atherosclerosis has not been elucidated. This study aimed to examine the roles of pharmacologically inhibiting EphA2 and the underlying mechanism in ameliorating atherosclerosis. ALW-II-41-27 was administered to apoE[-/-] mice fed a high-fat diet via intraperitoneal injection. We first discovered that ALW-II-41-27 led to a significant reduction in atherosclerotic plaques, evidenced by reduced lipid and macrophage accumulation, alongside an increase in collagen and smooth muscle cell content. ALW-II-41-27 also significantly lowered plasma and hepatic cholesterol levels, as well as the colonic inflammation. Furthermore, gut microbiota was analyzed by metagenomics and plasma metabolites by untargeted metabolomics. ALW-II-41-27-treated mice enriched Enterococcus, Akkermansia, Eggerthella and Lactobaccilus, accompanied by enhanced secondary bile acids production. To explore the causal link between ALW-II-41-27-associated gut microbiota and atherosclerosis, fecal microbiota transplantation was employed. Mice that received ALW-II-41-27-treated mouse feces exhibited the attenuated atherosclerotic plaque. In clinical, lower plasma DCA and HDCA levels were determined in CAD patients using quantitative metabolomics and exhibited a negative correlation with higher monocytes EphA2 expression. Our findings underscore the potential of ALW-II-41-27 as a novel therapeutic agent for atherosclerosis, highlighting its capacity to modulate gut microbiota composition and bile acid metabolism, thereby offering a promising avenue for CAD.},
}
@article {pmid39426960,
year = {2024},
author = {Zheng, M and Wen, L and He, C and Chen, X and Si, L and Li, H and Liang, Y and Zheng, W and Guo, F},
title = {Sequencing-guided re-estimation and promotion of cultivability for environmental bacteria.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {9051},
pmid = {39426960},
issn = {2041-1723},
support = {No. 31670492//National Natural Science Foundation of China (National Science Foundation of China)/ ; No. 32270006//National Natural Science Foundation of China (National Science Foundation of China)/ ; No. 2021J01027//Natural Science Foundation of Fujian Province (Fujian Provincial Natural Science Foundation)/ ; },
mesh = {*RNA, Ribosomal, 16S/genetics ; *Sewage/microbiology ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation &amp; purification/metabolism ; *Soil Microbiology ; Phylogeny ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; },
abstract = {The low cultivability of environmental bacteria has been widely acknowledged, but most previous estimates focused on the proportion of cultivable cells rather than cultivable taxa. Here, we estimate the proportions of cultivable cells and cultivable taxa for two sample types (soil and activated sludge) using cell counting, 16S rRNA gene amplicon sequencing, metagenomics, and cultivation on agar plates under various conditions. We find that the proportion of cultivable taxa exceeds that of cultivable cells at the sample level. A large proportion of cultivable taxa are taxonomically novel but tend to be present at very low abundance on agar plates, forming microcolonies, and some of them cease to grow during subculture. Compared with uncultivable taxa (under the conditions used in our study), cultivatable taxa tend to display higher metabolic activity as inferred by measuring rRNA copies per cell. Finally, we use the generated taxonomic and genomic information as a guide to isolate a strain representing a yet-uncultured class within the Bacteroidota and to enhance the cultivable diversity of Burkholderiales from activated sludge.},
}
@article {pmid39426578,
year = {2024},
author = {Tao, Y and Zeng, Y and Zeng, R and Gou, X and Zhou, X and Zhang, J and Nhamdriel, T and Fan, G},
title = {The total alkaloids of Berberidis Cortex alleviate type 2 diabetes mellitus by regulating gut microbiota, inflammation and liver gluconeogenesis.},
journal = {Journal of ethnopharmacology},
volume = {},
number = {},
pages = {118957},
doi = {10.1016/j.jep.2024.118957},
pmid = {39426578},
issn = {1872-7573},
abstract = {Type 2 diabetes mellitus (T2DM) has become a public health problem worldwide. There is growing interest in finding drugs to treat T2DM from herbal medicine. Berberidis Cortex is a traditional Tibetan herb commonly used in the treatment of T2DM, and alkaloids are its main active components. However, the anti-diabetic mechanisms of the total alkaloids of Berberidis Cortex (TBC) remain unclear.<br><br>AIM OF THE STUDY: The aim of this study was to evaluate the anti-T2DM efficacy of TBC and reveal the mechanisms behind its effects.<br><br>MATERIALS AND METHODS: UPLC-Q-Exactive Orbitrap MS technology was employed to qualitatively identify alkaloid components in TBC. T2DM rat models were induced by high-fat diet combined with streptozotocin, and then treated with different doses of TBC (43.5, 87, 174 mg/kg/d) for 40 days. Biochemical parameters, such as fasting blood glucose (FBG), oral glucose tolerance test (OGTT), glycated serum protein (GSP), homeostatic model assessment of insulin resistance (HOMA-IR), total cholesterol (TC), triglycerides (TG), and low-density lipoprotein cholesterol (LDL-C), alongside H&amp;E and PAS staining were used to evaluate the anti-diabetic activity of TBC. More importantly, metagenomics, transcriptomics, targeted metabolomics, and western blot analysis were integrated to reveal the underlying mechanisms of TBC for T2DM treatment.<br><br>RESULTS: TBC significantly reduced the levels of FBG, OGTT, GSP, HOMA-IR, TC, TG, and LDL-C, and improved the histopathological alterations of pancreatic and liver tissues in T2D rats. It also reduced serum levels of lipopolysaccharide (LPS) and several pro-inflammatory cytokines (IL-6, IL-1&#x3b2; and TNF-&#x3b1;). Gut microbiome analysis by metagenomics proved that TBC could improve gut microbiota dysbiosis, including an increase in some beneficial bacteria (e.g., Bifidobacterium pseudolongum and Lactobacillus acidophilus) and a decrease in some harmful bacteria (e.g., Marvinbryantia and Parabacteroides). Western blot analysis found that TBC significantly up-regulated the expression of three intestinal barrier related tight junction proteins (ZO-1, occludin, and claudin-1), and effectively suppressed several key proteins in the TLR4/MyD88/NF-&#x3ba;B inflammatory cascade, including TLR4, MyD88 and p-NF-&#x3ba;B p65. Moreover, hepatic transcriptomics analysis further revealed the regulatory role of TBC on gluconeogenesis related genes, such as Pgc, and Creb1. Targeted metabolomics and western blot analysis showed that TBC improved BAs dysregulation in T2DM rats, specifically increasing TCDCA and CA levels, thereby activating several proteins in the FXR/FGF15 signaling axis (i.e., FXR, FGF15 and FGFR4), and then decreased the expression of p-CREB1 and PGC-1&#x3b1; to inhibit liver gluconeogenesis.<br><br>CONCLUSIONS: TBC can significantly improve hyperglycemia, insulin resistance, hyperlipidemia, and inflammation in T2DM rats. The mechanism is related to the regulation of multiple links, including improving gut microbiota dysbiosis, protecting the intestinal barrier by up-regulating the expression of three tight junction proteins, reducing inflammation by inhibiting the LPS/TLR4/MyD88/NF-&#x3ba;B pathway, and inhibiting liver gluconeogenesis by regulating BAs/FXR/FGF15 and CREB1/PGC-1&#x3b1; signaling pathways.},
}
@article {pmid39426464,
year = {2024},
author = {Tang, Y and Liu, X and Zhu, S and Jia, M and Liu, JX and Sun, HZ},
title = {New insights into the enteric methane production based on the archaeal genome map of ruminant gastrointestinal tract.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2024.09.016},
pmid = {39426464},
issn = {2090-1224},
abstract = {INTRODUCTION: As one of the important components of ruminant gastrointestinal tract (GIT) microbiome, archaea are involved in many biological processes, especially methanogenesis. However, the diversity and individual metabolic characteristics of archaea in this habitat remain largely understudied, partly due to the lack of a unified reference genome catalog.<br><br>OBJECTIVES: This study aimed to construct a unified genome map for taxonomic and functional exploration of ruminant GIT archaea in the future.<br><br>METHODS: We collected archaeal genomes from public sources and new data of this study. We performed phylogenetic analysis, functional genomics analyses, prophages identification based on the genomes. Using collected genomes as a reference, we conducted metagenomic and metatranscriptomic analyses on rumen fluid samples from 18 dairy cows with different methane (CH4) production.<br><br>RESULTS: We constructed the ruminant GIT archaeal genomes (RGAG) by compiling 405 strain-level (160 species) non-redundant archaeal genomes from more than 10 ruminant species. The functional heterogeneity and methanogenic structure within RGAG was investigated. RGAG possessed 1,124 (99.5&#x202f;%) unknown microbial biosynthetic gene clusters. A survey of RGAG-borne prophages identified 63 prophages with 122 host-beneficial genes and 18 auxiliary metabolic genes (AMGs). The pipeline for both metagenomics and metatranscriptomics generated in the study revealed the roles of archaeal genomes under-assessed in general analyses of muti-omics. The highly expressed genus Methanosphaera was negatively correlated with CH4 production.<br><br>CONCLUSION: A unified genome map of ruminant GIT archaea is constructed in the study. Functional genomics indicates that the multifaceted functions of RGAG remains undiscovered. Multi-omics analyses reveals the advantages of metatranscriptomics over metagenomics in studying rumen archaeal communities. Differences in rumen archaeal community structure among cattle with different CH4 production may reflect the balance between rumen hydrogen production and methanogenesis. Our work provides new understanding of archaeal functions in the ruminant GIT and potential targets for future CH4 reduction.},
}
@article {pmid39426111,
year = {2024},
author = {Shang, KM and Elsheikha, HM and Ma, H and Wei, YJ and Zhao, JX and Qin, Y and Li, JM and Zhao, ZY and Zhang, XX},
title = {Metagenomic profiling of cecal microbiota and antibiotic resistome in rodents.},
journal = {Ecotoxicology and environmental safety},
volume = {286},
number = {},
pages = {117186},
doi = {10.1016/j.ecoenv.2024.117186},
pmid = {39426111},
issn = {1090-2414},
abstract = {The rodent gut microbiota is a known reservoir of antimicrobial resistance, yet the distribution of antibiotic resistance genes (ARGs) within rodent cecal microbial communities and the specific bacterial species harboring these ARGs remain largely underexplored. This study employed high-throughput sequencing of 122 samples from five distinct rodent species to comprehensively profile the diversity and distribution of ARGs and to identify the bacterial hosts of these genes. A gene catalog of the rodent cecal microbiome was constructed, comprising 22,757,369 non-redundant genes. Analysis of the microbial composition and diversity revealed that Bacillota and Bacteroidota were the dominant bacterial phyla across different rodent species, with significant variations in species composition among the rodents. In total, 3703 putative antimicrobial resistance protein-coding genes were identified, corresponding to 392 unique ARG types classified into 32 resistance classes. The most enriched ARGs in the rodent cecal microbiome were associated with multidrug resistance, followed by glycopeptide and elfamycin antibiotics. Procrustes analysis demonstrated a correlation between the structure of the microbial community and the resistome. Metagenomic assembly-based host tracking indicated that most ARG-carrying contigs originated from the bacterial family Oscillospiraceae. Additionally, 130 ARGs showed significant correlations with mobile genetic elements. These findings provide new insights into the cecal microbiota and the prevalence of ARGs across five rodent species. Future research on a wider range of wild rodent species carrying ARGs will further elucidate the mechanisms underlying the transmission of antimicrobial resistance.},
}
@article {pmid39425237,
year = {2024},
author = {Zelasko, S and Swaney, MH and Sandstrom, S and Davenport, TC and Seroogy, CM and Gern, JE and Kalan, LR and Currie, CR},
title = {Upper respiratory microbial communities of healthy populations are shaped by niche and age.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {206},
pmid = {39425237},
issn = {2049-2618},
support = {F30AI169759/NH/NIH HHS/United States ; T32AI055397/NH/NIH HHS/United States ; U19AI104317/NH/NIH HHS/United States ; U19AI104317/NH/NIH HHS/United States ; U19AI142720/NH/NIH HHS/United States ; U19AI142720/NH/NIH HHS/United States ; },
mesh = {Humans ; *Microbiota ; *Mouth/microbiology ; Adult ; Infant ; Female ; *Bacteria/classification/genetics/isolation &amp; purification ; Male ; Age Factors ; Child, Preschool ; Healthy Volunteers ; Metagenomics/methods ; Respiratory System/microbiology ; Metagenome ; },
abstract = {BACKGROUND: Alterations in upper respiratory microbiomes have been implicated in shaping host health trajectories, including by limiting mucosal pathogen colonization. However, limited comparative studies of respiratory microbiome development and functioning across age groups have been performed. Herein, we perform shotgun metagenomic sequencing paired with pathogen inhibition assays to elucidate differences in nasal and oral microbiome composition and intermicrobial interactions across healthy 24-month-old infant (n = 229) and adult (n = 100) populations.<br><br>RESULTS: We find that beta diversity of nasal and oral microbiomes varies with age, with nasal microbiomes showing greater population-level variation compared to oral microbiomes. Infant microbiome alpha diversity was significantly lower across nasal samples and higher in oral samples, relative to adults. Accordingly, we demonstrate significant differences in genus- and species-level composition of microbiomes between sites and age groups. Antimicrobial resistome patterns likewise varied across body sites, with oral microbiomes showing higher resistance gene abundance compared to nasal microbiomes. Biosynthetic gene clusters encoding specialized metabolite production were found in higher abundance across infant oral microbiomes, relative to adults. Investigation of pathogen inhibition revealed greater inhibition of gram-negative and gram-positive bacteria by oral commensals, while nasal isolates had higher antifungal activity.<br><br>CONCLUSIONS: In summary, we identify significant differences in the microbial communities inhabiting nasal and oral cavities of healthy infants relative to adults. These findings inform our understanding of the interactions impacting respiratory microbiome composition and functions related to colonization resistance, with important implications for host health across the lifespan. Video Abstract.},
}
@article {pmid39425038,
year = {2024},
author = {Woldeyohannis, NN and Desta, AF},
title = {Metagenome-based microbial community analysis of urine-derived fertilizer.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {418},
pmid = {39425038},
issn = {1471-2180},
mesh = {Humans ; *Fertilizers/analysis ; *Urine/microbiology ; *Bacteria/genetics/classification/isolation &amp; purification ; *Struvite ; *Metagenome ; Microbiota/genetics ; Metagenomics/methods ; DNA, Bacterial/genetics ; Phylogeny ; },
abstract = {Phosphorus is essential for food production and its supply is limited. Urine is an excellent source of phosphorus and one way to produce fertilizer is through conversion of urine to struvite (MgNH3PO4.6H2O). The present study aimed to understand the bacterial portion of the microbial community composition and dynamics of plasmid-mediated antimicrobial resistant genes during the optimized process of struvite production from composite human urine. Samples for DNA extraction was collected from fresh urine, stored urine and struvite during the process of struvite production. Shotgun metagenomic analysis was employed to understand the bacterial community. The most dominant phyla in the fresh and stored urine samples were Pseudomonadata, which comprised of 60% and 43% respectively, followed by Bacillota, comprised of 25% and 39% respectively. The struvite sample was dominated by the phylum Bacilliota (61%), Pseudomonadota (18%) and bacteroidota (12%). Members of the above phyla persisted in dominating each sample accordingly. Member of the family Morganellaceae was dominant in the fresh sample while the stored urine and struvite samples were dominated by the family Clostridiaceae. A decrease of members of the class Gammaproteobacteria was observed from the fresh to the struvite sample though not statistically significant. The genus Pseudomonas remained to be the most dominant member of Gammaproteobacteria in the fresh and stored urine sample with OTU count of 12,116 and 6,155 with a marked decrease by half in the stored sample. On the other hand, members of the genera Clostridium, Enterococcus, Bacteroides in the stored samples and Clostridium, Alkaliphilus and Pseudomonas in the struvite samples were dominant. 96% of the identified genera were shared in all the samples and the antimicrobial resistance genes (ARGs) identified in the fresh urine were shared by the struvite but not by the stored urine (e.g. sul, cat, aph and aac members). The presence of high abundance of ARGs in struvite needs attention in the persistence and transmissibility of the ARGs before application for agriculture.},
}
@article {pmid39424897,
year = {2024},
author = {Jia, X and Wang, W and Wu, M and Pang, L and Yang, C and Ling, Y and Yi, Z and Zhang, X},
title = {Empirical assessment of the enrichment-based metagenomic methods in identifying diverse respiratory pathogens.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {24493},
pmid = {39424897},
issn = {2045-2322},
support = {81801991//the National Natural Science Foundation of China/ ; GW VI-11.1-09//three-Year Initiative Plan for Strengthening Public Health System Construction in Shanghai/ ; GWVI-2.2//three-Year Initiative Plan for Strengthening Public Health System Construction in Shanghai/ ; GWVI-11.1-15//three-Year Initiative Plan for Strengthening Public Health System Construction in Shanghai/ ; 20Y11911300//the 2020 Shanghai Science and Technology Innovation Action Plan Medical Innovation Research Special Project/ ; SHDC12022121//the Shanghai Hospital Development Center Foundation/ ; 2017ZX10103009-001//the National Science and Technology Major Project of China/ ; 2018ZX10305409-001-005//the National Science and Technology Major Project of China/ ; },
mesh = {*Metagenomics/methods ; Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Respiratory Tract Infections/microbiology/virology/diagnosis ; Bacteria/genetics/isolation &amp; purification/classification ; Metagenome ; Viruses/genetics/isolation &amp; purification/classification ; },
abstract = {Probe-based nucleic acid enrichment represents an effective route to enhance the detection capacity of next-generation sequencing (NGS) in a set of clinically diverse and relevant microbial species. In this study, we assessed the effect of the enrichment-based sequencing on identifying respiratory infections using tiling RNA probes targeting 76 respiratory pathogens and sequenced using both Illumina and Oxford Nanopore platforms. Forty respiratory swab samples pre-tested for a panel of respiratory pathogens by qPCR were used to benchmark the sequencing data. We observed a general improvement in sensitivity after enrichment. The overall detection rate increased from 73 to 85% after probe capture detected by Illumina. Moreover, enrichment with probe sets boosted the frequency of unique pathogen reads by 34.6 and 37.8-fold for Illumina DNA and cDNA sequencing, respectively. This also resulted in significant improvements on genome coverage especially in viruses. Despite these advantages, we found that library pooling may cause reads mis-assignment, probably due to crosstalk issues arise from post-capture PCR and from pooled sequencing, thus increasing the risk of bleed-through signal. Taken together, an overall improvement in the breadth and depth of pathogen coverage is achieved using enrichment-based sequencing method. For future applications, automated library processing and pooling-free sequencing could enhance the precision and timeliness of probe enrichment-based clinical metagenomics.},
}
@article {pmid39424349,
year = {2024},
author = {Zhang, Y and Wang, Z and Wang, F and Zhou, H and Zhang, L and Xie, B},
title = {Anaerobic Degradation of Aromatic and Aliphatic Biodegradable Plastics: Potential Mechanisms and Pathways.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c07554},
pmid = {39424349},
issn = {1520-5851},
abstract = {Biodegradable plastics (BDPs) have been widely used as substitutes for traditional plastics, and their environmental fate is a subject of intense research interest. Compared with the aerobic degradation of BDPs, their biodegradability under anaerobic conditions in environmental engineering systems remains poorly understood. This study aimed to investigate the degradability of BDPs composed of poly(butylene adipate-co-terephthalate) (PBAT), poly(lactide acid) (PLA), and their blends, and explore the mechanism underlying their microbial degradation under conditions of anaerobic digestion (AD). The BDPs readily depolymerized under thermophilic conditions but were hydrolyzed at a slow rate under conditions of mesophilic AD. After 45 days of thermophilic AD, a decrease in the molecular weight and significant increase in the production of methane and carbon dioxide production were observed. Network and metagenomics analyses identified AD as reservoirs of plastic-degrading bacteria that produce multiple plastic-degrading enzymes. PETase was identified as the most abundant plastic-degrading enzyme. A potential pathway for the anaerobic biodegradation of BDPs was proposed herein. The polymers of high molecular weight were subjected to abiotic hydrolysis to form oligomers and monomers, enabling subsequent microbial hydrolysis and acetogenesis. Ultimately, complete degradation was achieved predominantly via the pathway involved in the conversion of acetic acid to methane. These findings provide novel insight into the mechanism underlying the anaerobic degradation of BDPs and the microbial resources crucial for the efficient degradation of BDPs.},
}
@article {pmid39424030,
year = {2024},
author = {Wan, P and Liu, Y and Li, B and Yu, X and Jiang, L and Lv, W},
title = {Yeast-enhanced activated sludge for improved nitrogen removal in wastewater treatment: Focus on dissolved organic nitrogen degradation.},
journal = {Environmental research},
volume = {},
number = {},
pages = {120181},
doi = {10.1016/j.envres.2024.120181},
pmid = {39424030},
issn = {1096-0953},
abstract = {Dissolved organic nitrogen (DON) in effluent of wastewater treatment plants (WWTP), particularly hydrophilic DON, is usually more effective than dissolved inorganic nitrogen (DIN) in stimulating phytoplankton growth and increases the risk of eutrophication in receiving waterbodies. Proteins, amino acids, and nucleic acids, which are the main sources of DON in the effluent, are produced during the hydrolysis of extracellular polymeric substances (EPS) in activated sludge. Herein, a yeast strain Candida tropicalis O2, which was highly efficient in degrading DON in EPS was screened. Within 48-hour batch experiments, the DON removal rates of the extracted hydrophilic and hydrophobic EPS reached 68.26% and 59.27%, respectively. During the continuous 35-day operation of sequencing batch bioreactor (SBR) fed with synthetic wastewater, the yeast-enhanced activated sludge (AS-Y) reactor demonstrated a marked improvement in removing various pollutants compared to the traditional activated sludge (AS) reactor. Specifically, DON removal increased by 1.53 mg/L (24.75%), hydrophilic DON by 1.24 mg/L (27.13%), hydrophobic DON by 0.28 mg/L (12.08%), and COD removal by 4.04 mg/L (6.48%). Although the DIN removal decreased by 0.38 mg/L (3.86%), it did not attenuate the overall TN removal from the system, and an additional TN reduction of 1.15 mg/L (7.13%) was achieved. Metagenomic analysis showed that adding strain O2 slightly inhibited the DIN metabolism, and the relative abundances of napB, nirK/S, norB/C, and nosZ involved in denitrification somewhat decreased. Kyoto Encyclopedia of Genes and Genomes and Carbohydrate-Active Enzymes annotations revealed that adding strain O2 promoted amino acid and carbohydrate metabolism. The increased relative abundance of Candida indicated that strain O2 was able to colonize the sludge in AS-Y reactor, which was conducive to synergistic interactions with other microorganisms. This study provided a novel method for in situ improving nitrogen removal in WWTP and reducing the eutrophication risk of the effluent to receiving waterbodies.},
}
@article {pmid39423892,
year = {2024},
author = {Ouyang, W and Huang, Y and Li, C and Huang, W and Yuan, S and Liu, H},
title = {Control of dissolved H2 concentration enhances electron generation, transport and TCE reduction by indigenous microbial community.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {177014},
doi = {10.1016/j.scitotenv.2024.177014},
pmid = {39423892},
issn = {1879-1026},
abstract = {Electrokinetic enhanced bioremediation (EK-Bio) is practical for trichloroethene (TCE) dechlorination because the cathode can produce a wide range of dissolved H2 (DH) concentrations of 1.3-0 mg/L from the electrode to the aquifer. In this study, TCE dechlorination was investigated under different DH concentrations. The mechanisms were discussed by analyzing the microbial community structure and abundance of organohalide-respiring bacteria (OHRB) using 16S rRNA, and the gene abundances of key enzymes in the TCE electron transport chain using metagenomic analysis. The results showed that the moderate DH concentration of 0.19-0.53 mg/L exhibited the most pronounced TCE dechlorination, even better than the higher DH concentrations, due to the optimal redox environment, the enrichments of OHRB, reductive dehalogenase (rdhA) genes and key enzyme genes in the electron generation and transport chain. More electrons were obtained from H2 metabolism by Dehalobacter by promoting the formation of [NiFe] hydrogenase (HupS/L/C) or from glycolysis by versatile OHRB by stimulating the formation of formate and enriching formate dehydrogenase (FDH) under moderate DH conditions. In addition, the enhanced amino acid metabolism improved the vitamin K cycle for electron transport and enriched the reductive dechlorinating enzyme (RDase) genes. This study identifies the optimal DH concentration that facilitates bioremediation efficiency, provides insights into microbial community shifts and key enzymatic pathways in EK-Bio remediation.},
}
@article {pmid39423786,
year = {2024},
author = {Ren, H and Wang, R and Ying, L and Iyobosa, E and Chen, G and Zang, D and Tong, M and Li, E and Nerenberg, R},
title = {Removal of sulfamethoxazole in an algal-bacterial membrane aerated biofilm reactor: Microbial responses and antibiotic resistance genes.},
journal = {Water research},
volume = {268},
number = {Pt A},
pages = {122595},
doi = {10.1016/j.watres.2024.122595},
pmid = {39423786},
issn = {1879-2448},
abstract = {Antibiotics are frequently detected in wastewater, but often are poorly removed in conventional wastewater treatment processes. Combining microalgal and nitrifying bacterial processes may provide synergistic removal of antibiotics and ammonium. In this research, we studied the removal of the antibiotic sulfamethoxazole (SMX) in two different reactors: a conventional nitrifying bacterial membrane aerated biofilm reactor (bMABR) and algal-bacterial membrane aerated biofilm reactor (abMABR) systems. We investigated the synergistic removal of antibiotics and ammonium, antioxidant activity, microbial communities, antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and their potential hosts. Our findings show that the abMABR maintained a high sulfamethoxazole (SMX) removal efficiency, with a minimum of 44.6 % and a maximum of 75.8 %, despite SMX inhibition, it maintained a consistent 25.0 % ammonium removal efficiency compared to the bMABR. Through a production of extracellular polymeric substances (EPS) with increased proteins/polysaccharides (PN/PS), the abMABR possibly allowed the microalgae-bacteria consortium to protect the bacteria from SMX inactivation. The activity of antioxidant enzymes caused by SMX was reduced by 62.1-98.5 % in the abMABR compared to the bMABR. Metagenomic analysis revealed that the relative abundance of Methylophilus, Pseudoxanthomonas, and Acidovorax in the abMABR exhibited a significant positive correlation with SMX exposure and reduced nitrate concentrations and SMX removal. Sulfonamide ARGs (sul1 and sul2) appeared to be primarily responsible for defense against SMX stress, and Hyphomicrobium and Nitrosomonas were the key carriers of ARGs. This study demonstrated that the abMABR system has great potential for removing SMX and reducing the environmental risks of ARGs.},
}
@article {pmid39423213,
year = {2024},
author = {Ma, J and Yang, X and He, J},
title = {Comprehensive gut microbiota composition and microbial interactions among the three age groups.},
journal = {PloS one},
volume = {19},
number = {10},
pages = {e0305583},
doi = {10.1371/journal.pone.0305583},
pmid = {39423213},
issn = {1932-6203},
mesh = {Humans ; *Gastrointestinal Microbiome ; Aged ; Aged, 80 and over ; Adult ; Middle Aged ; Male ; Aging ; Young Adult ; Microbial Interactions ; Female ; Bacteria/genetics/classification ; Age Factors ; Archaea/genetics ; },
abstract = {There is a growing interest in studying the microbiota associated with aging by integrating multiple longevity researches while minimizing the influence of confounding factors. Here, we reprocessed metagenomic sequencing data from four different aging research studies and evaluated potential confounding factors in order to minimize the batch effect. Subsequently, we detected the diversity and abundance of the gut microbiome in three different age cohorts. Out of 1053 different bacteria species, only four showed substantial depletion across different age groups: Ligilactobacillus ruminis, Turicibacter sp. H121, Blautia massiliensis, and Anaerostipes hadrus. Archaea accumulated more in young individuals compared to elderly and centenarians. Candida albicans was more prevalent in centenarians, but Nakaseomyces glabratus (also known as Candida glabrata) was more common in elderly adults. Shuimuvirus IME207 showed a significant increase in centenarians compared to both control groups. In addition, we utilized a Fisher's exact test to investigate topological properties of differentially abundant microbiota in the co-occurrence network of each age group. Microbial signatures specific to different age stages were identified based on the condition: the reads showing differential abundance were higher compared to the other age groups. Lastly, we selected Methanosarcina sp. Kolksee for the Y group, Prevotella copri for the E group and Shuimuvirus IME207 for the C group as representatives of age-related characteristics to study how their interactions change during the aging process. Our results provide crucial insights into the gut microbiome's ecological dynamics in relation to the aging process.},
}
@article {pmid39422492,
year = {2024},
author = {Lu, F and Huang, T and Chen, R and Yin, H},
title = {Multi-omics analysis reveals the interplay between pulmonary microbiome and host in immunocompromised patients with sepsis-induced acute lung injury.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0142424},
doi = {10.1128/spectrum.01424-24},
pmid = {39422492},
issn = {2165-0497},
abstract = {UNLABELLED: The mechanisms behind the high inflammatory state and immunocompromise in severe sepsis remain unclear. While microbiota's role in immune regulation is known, the impact of pulmonary microbiota on sepsis progression is not fully understood. This study aims to investigate pulmonary microbial characteristics in septic patients and their relationship with host immune-related genes and clinical features. Fifty-four sepsis patients were divided into the immunocompromised host (ICH) group (n = 18) and the control group (n = 36). Bronchoalveolar lavage fluid (BALF) was analyzed using metagenomic next-generation sequencing (mNGS) to assess the pulmonary microbiome, and transcriptomic sequencing evaluated host gene expression. The pulmonary microbiota network in the ICH group showed notable alterations. Symbiotic bacteria like Streptococcus salivarius and Streptococcus oralis were key taxa in the control group. In contrast, opportunistic pathogens such as Campylobacter concisus and Prevotella melaninogenica, typically linked to infections in various body sites, dominated in the ICH group. Transcriptomic analysis revealed differential genes between the two groups. The downregulated differential genes in the ICH group were primarily enriched in pathways related to T-cell activation and the Type I interferon signaling pathway, both crucial for the immune system. Further correlation analysis identified significant associations between certain microbes and host genes, as well as clinical indicators, particularly with species like Campylobacter concisus, Streptococcus salivarius, Streptococcus oralis, and several species of Veillonella. These findings suggest that alterations in the pulmonary microbiome, especially the presence of opportunistic pathogens, may contribute to immune dysregulation in immunocompromised septic patients, warranting further research to explore causal relationships.<br><br>IMPORTANCE: Recent research has substantiated the significant role of microbiota in immune regulation, which could influence high inflammatory state and immunocompromise in patients with severe sepsis, as well as provide new opportunities for acute lung injury induced by sepsis diagnosis and treatment. Our study identified some potential critical microbes (Campylobacter concisus and several species of Veillonella), which were correlated with immune-related genes and might be the novel target to regulate immunotherapy in sepsis.},
}
@article {pmid39422474,
year = {2024},
author = {Zhu, Q and Huang, S and Gonzalez, A and McGrath, I and McDonald, D and Haiminen, N and Armstrong, G and Vázquez-Baeza, Y and Yu, J and Kuczynski, J and Sepich-Poore, GD and Swafford, AD and Das, P and Shaffer, JP and Lejzerowicz, F and Belda-Ferre, P and Havulinna, AS and Méric, G and Niiranen, T and Lahti, L and Salomaa, V and Kim, H-C and Jain, M and Inouye, M and Gilbert, JA and Knight, R},
title = {Correction for Zhu et al., "Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy".},
journal = {mSystems},
volume = {},
number = {},
pages = {e0128924},
doi = {10.1128/msystems.01289-24},
pmid = {39422474},
issn = {2379-5077},
}
@article {pmid39422129,
year = {2024},
author = {Kanti Nath, B and Gupta, SD and Talukder, S and Tonu, NS and Raidal, SR and Forwood, JK and Sarker, S},
title = {Metagenomic Detection of Multiple Viruses in Monk Parakeet (Myiopsitta monachus) in Australia.},
journal = {Veterinary medicine and science},
volume = {10},
number = {6},
pages = {e70083},
doi = {10.1002/vms3.70083},
pmid = {39422129},
issn = {2053-1095},
mesh = {Animals ; *Feces/virology/microbiology ; *Parakeets/virology ; Bird Diseases/virology/epidemiology/microbiology ; Australia ; Adenoviridae/isolation &amp; purification/classification/genetics ; Parvoviridae/isolation &amp; purification/genetics/classification ; Phylogeny ; Circovirus/genetics/isolation &amp; purification/classification ; High-Throughput Nucleotide Sequencing/veterinary ; Victoria ; Circoviridae/isolation &amp; purification/genetics/classification ; Virome ; Metagenomics ; },
abstract = {BACKGROUND: Birds are known to harbour many pathogens, including circovirus, herpesviruses, adenoviruses and Chlamydia psittaci. Some of these pose zoonotic risks, while others, such as beak and feather disease virus (BFDV), have a significant impact on the conservation of endangered bird species.<br><br>OBJECTIVES: This study was aimed to determine the faecal virome of a group of apparently healthy Monk parakeet using high-throughput sequencing.<br><br>METHODS: Fresh faecal samples were collected from four Monk parakeets at a pet shop in Melbourne, Australia. Virus enrichment and nucleic acid extraction were performed on the faecal samples, followed by high-throughput sequencing at the Australian Genome Research Facility (AGRF).<br><br>RESULTS: Utilising an established pipeline for high-throughput sequencing data analysis, this study revealed the presence of three viruses of the families Circoviridae, Parvoviridae and Adenoviridae. Subsequent sequence comparison and phylogenetic analyses further confirmed that the detected viruses belong to the genera Chaphamaparvovirus (unassigned species), Circovirus (species Circovirus parrot) and Siadenovirus (species Siadenovirus viridis).<br><br>CONCLUSION: Despite non-pathogenicity, the existence of multiple viruses within a bird species underscores the risk of these viruses spreading into the pet trade. Detection and a better understanding of avian viruses are crucial for the establishment of appropriate management and biosecurity measures in the domestic and international bird trade, which ultimately supports the conservation of vulnerable bird species.},
}
@article {pmid39421628,
year = {2024},
author = {Shaykhutdinov, IH and Iliasov, PV and Limareva, LV and Sustretov, AS and Kokorev, DA and Sokolov, AV},
title = {Biomineralization of Human Genomic DNA into ZIF-8, a Zeolite-Like Metal-Organic Framework.},
journal = {Sovremennye tekhnologii v meditsine},
volume = {16},
number = {1},
pages = {5-13},
pmid = {39421628},
issn = {2309-995X},
mesh = {Humans ; *Metal-Organic Frameworks/chemistry ; *DNA ; *Zeolites/chemistry ; Biomineralization ; Genome, Human ; Imidazoles/chemistry ; },
abstract = {UNLABELLED: The aim of the study was to assess the capabilities of human genomic DNA biomineralization into ZIF-8 metal-organic framework (MOF) preserving DNA sequence integrity after the encapsulation cycle and composite dissolving. The study is an initial stage of the project aimed at developing an abiotic vector to be used when working with native nucleic acids of an arbitrary size based on DNA@ZIF-8 composite.<br><br>MATERIALS AND METHODS: We studied human genomic DNA isolated from lymphocytes of peripheral blood of healthy volunteers using Proba-NK kit (DNA-Technology LLC, Russia). Genomic DNA purity and concentration was estimated spectrophotometrically at 260/280 nm using Tecan Infinity 200 Pro plate reader (Tecan Instruments, Austria). ZIF-8 was synthesized in the physiological conditions (37&#xb0;C) by mixing zinc salt and 2-methylimidazole aqueous solutions at different molar ratios. Human genomic DNA was encapsulated into ZIF-8 in similar conditions. The obtained MOF and DNA@ZIF-8 composite were studied using X-ray powder diffraction at the Phaser D2 XRPD device (Bruker, USA), and the specific surface area was estimated using Autosorb iQ porosimetry analyzer (Quantachrome, USA). The encapsulated DNA was quantified by dissolving DNA@ZIF-8 composite in the citrate buffer. DNA integrity was assessed by real-time allele-specific PCR (AS-PCR) using the kits for single nucleotide polymorphisms (Lytech, Russia) at the Quantstudio 6 Pro PCR machine (Thermo Scientific, USA). In case of using the kits with electrophoretic detection, the amplification was performed on the thermal cycler T100 (Thermo Scientific, USA).<br><br>RESULTS: The polymer ZIF-8 and DNA@ZIF-8 composite were obtained at different molar ratios of zinc ions and 2-methylimidazole. We characterized their structure and specific surface area. Genomic DNA biomineralization efficacy was found to be about 7-8%. PCR indicated the integrity of non-selectively chosen loci within the biomineralized DNA.<br><br>CONCLUSION: The study confirmed the possibility of human genomic DNA encapsulation into ZIF-8 metal-organic framework. After the biomineralization, DNA was found to preserve feasibility to be used in studies to investigate genetic constructs.},
}
@article {pmid39421601,
year = {2024},
author = {Dopson, M and Rezaei Somee, M and González-Rosales, C and Lui, LM and Turner, S and Buck, M and Nilsson, E and Westmeijer, G and Ashoor, K and Nielsen, TN and Mehrshad, M and Bertilsson, S},
title = {Novel candidate taxa contribute to key metabolic processes in Fennoscandian Shield deep groundwaters.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae113},
pmid = {39421601},
issn = {2730-6151},
abstract = {The continental deep biosphere contains a vast reservoir of microorganisms, although a large proportion of its diversity remains both uncultured and undescribed. In this study, the metabolic potential (metagenomes) and activity (metatranscriptomes) of the microbial communities in Fennoscandian Shield deep subsurface groundwaters were characterized with a focus on novel taxa. DNA sequencing generated 1270 de-replicated metagenome-assembled genomes and single-amplified genomes, containing 7 novel classes, 34 orders, and 72 families. The majority of novel taxa were affiliated with Patescibacteria, whereas among novel archaea taxa, Thermoproteota and Nanoarchaeota representatives dominated. Metatranscriptomes revealed that 30 of the 112 novel taxa at the class, order, and family levels were active in at least one investigated groundwater sample, implying that novel taxa represent a partially active but hitherto uncharacterized deep biosphere component. The novel taxa genomes coded for carbon fixation predominantly via the Wood-Ljungdahl pathway, nitrogen fixation, sulfur plus hydrogen oxidation, and fermentative pathways, including acetogenesis. These metabolic processes contributed significantly to the total community's capacity, with up to 9.9% of fermentation, 6.4% of the Wood-Ljungdahl pathway, 6.8% of sulfur plus 8.6% of hydrogen oxidation, and energy conservation via nitrate (4.4%) and sulfate (6.0%) reduction. Key novel taxa included the UBA9089 phylum, with representatives having a prominent role in carbon fixation, nitrate and sulfate reduction, and organic and inorganic electron donor oxidation. These data provided insights into deep biosphere microbial diversity and their contribution to nutrient and energy cycling in this ecosystem.},
}
@article {pmid39421252,
year = {2024},
author = {Klaassens, ES and Baak, ML and Mekkes, NJ and Bongoni, R and Schaubeck, M},
title = {Effect of protein modification in synbiotic infant formula on probiotic metabolic activity and bacterial composition in an infant gut-model.},
journal = {Microbiome research reports},
volume = {3},
number = {3},
pages = {38},
pmid = {39421252},
issn = {2771-5965},
abstract = {Aim: Microbial colonization of the neonatal gut is pivotal in priming the infant's immune system. Human milk (HM) is the best nutrition for infants and supports the development of the microbiota due to prebiotic compounds and probiotic microorganisms. When exclusive breastfeeding is not possible, infant formula (IF) with probiotics is a strategy to support the infant's microbiome development. However, knowledge about the effects of the infant gut microbiota and different compounds in IF on individual probiotic strains is limited, as strain-level detection in a complex ecosystem is challenging. The aim of the present study was to show the effects of IF with different protein forms on the metabolic activity of two probiotic strains isolated from HM in a complex ecosystem. Methods: By using an ex-vivo infant gut model containing infant donor-microbiota, the effects of IF with either intact or extensively hydrolyzed protein on the metabolic activity of the donor microbiota, as well as two probiotic strains [Limosilactobacillus fermentum (L. fermentum) CECT 5716 (Lf) and Bifidobacterium breve (B. breve) DSM 32583 (Bb)], were analyzed. A new bioinformatic pipeline combined with a specific infant microbiome database was used to explore shotgun metagenome datasets (1200 Megabases) for taxonomic identification and strain-level tracking. Results: Both protein forms (i.e., intact or extensively hydrolyzed protein) in IF supported infant gut microbial metabolic activity equally, as evidenced by similar levels of short-chain fatty acids (SCFAs). Interestingly, gut microbial metabolic activity was found to be differently activated in a strain-dependent manner. Taxonomic profiling of the microbiome at the strain level enabled monitoring of the prevalence and abundance of both probiotic strains, even in a complex ecosystem. Conclusion: Food matrix and host microbiota interactions should be considered when evaluating strain-specific probiotic effects in the future.},
}
@article {pmid39421249,
year = {2024},
author = {Mueller, KD and Panzetta, ME and Davey, L and McCann, JR and Rawls, JF and Flores, GE and Valdivia, RH},
title = {Pangenomic analysis identifies correlations between Akkermansia species and subspecies and human health outcomes.},
journal = {Microbiome research reports},
volume = {3},
number = {3},
pages = {33},
pmid = {39421249},
issn = {2771-5965},
abstract = {Aim: Akkermansia are common members of the human gastrointestinal microbiota. The prevalence of these mucophilic bacteria, especially Akkermansia muciniphila (A. muciniphila), correlates with immunological and metabolic health. The genus Akkermansia in humans includes species with significantly larger genomes than A. muciniphila, leading us to postulate that this added genetic content may influence how they impact human metabolic and immunological health. Methods: We conducted a pangenomic analysis of 234 Akkermansia complete or near-complete genomes. We also used high-resolution species and subspecies assignments to reanalyze publicly available metagenomic datasets to determine if there are relationships between Akkermansia species and A. muciniphila clades with various disease outcomes. Results: Analysis of genome-wide average nucleotide identity, 16S rRNA gene identity, conservation of core Akkermansia genes, and analysis of the fatty acid composition of representative isolates support the partitioning of the genus Akkermansia into several species. In addition, A. muciniphila sensu stricto, the most prevalent Akkermansia species in humans, should be subdivided into two subspecies. For a pediatric cohort, we observed species-specific correlations between Akkermansia abundance with baseline obesity or after various interventions. For inflammatory bowel disease cohorts, we identified a decreased abundance of Akkermansia in patients with ulcerative colitis or Crohn's disease, which was species and subspecies-dependent. In patients undergoing immune checkpoint inhibitor therapies for non-small cell lung carcinoma, we observed a significant association between one A. muciniphila subspecies and survival outcomes. Conclusion: Our findings suggest that the prevalence of specific Akkermansia species and/or subspecies can be crucial in evaluating their association with human health, particularly in different disease contexts, and is an important consideration for their use as probiotics.},
}
@article {pmid39420944,
year = {2024},
author = {Chen, X and Zou, T and Ding, G and Jiang, S},
title = {Findings and methodologies in oral phageome research: a systematic review.},
journal = {Journal of oral microbiology},
volume = {16},
number = {1},
pages = {2417099},
pmid = {39420944},
issn = {2000-2297},
abstract = {BACKGROUND: The oral microbiome serves as both an indicator and a mediator of oral health. Evidence indicates that bacteriophages (phages) are widely present in the oral microbiome and exhibit diverse classifications and interactions with human cells and other microbes. These phages constitute the oral phageome, which potentially exerts significant yet unexplored effects on the interplay between oral and general health.<br><br>METHODS: Three databases (PubMed/MEDLINE, Embase and Scopus) were searched for metagenomic analyses that investigated the oral phageome. Eligible studies were synthesized based on their methodological approaches and findings.<br><br>RESULTS: A total of 14 articles were included in this systematic review. Among the 14 articles included, there were six studies that discussed disease-related alterations, along with a discursive examination of additional variables such as sampling niches, external interventions and methodologies. The phages that infect Streptococcus Actinomyces Haemophilus, and Veillonella have been discovered to be associated with chronic periodontitis, caries, and pancreatic ductal carcinoma.<br><br>CONCLUSIONS: This systematic review focuses on findings and methodologies in oral phageome studies, which were conducted using highly heterogeneous methodologies that explored the oral phageome in multiple directions while placing constraints on quantitative statistics. Combining different kinds of sample types, utilizing the characteristics of different methods, involving both DNA and RNA phages, and differentiating lysogenic and lytic phages should be the distinction of further studies.},
}
@article {pmid39420836,
year = {2024},
author = {Qu, W and Xu, Y and Yang, J and Shi, H and Wang, J and Yu, X and Chen, J and Wang, B and Zhuoga, D and Luo, M and Liu, R},
title = {Berberine alters the gut microbiota metabolism and impairs spermatogenesis.},
journal = {Acta biochimica et biophysica Sinica},
volume = {},
number = {},
pages = {},
doi = {10.3724/abbs.2024174},
pmid = {39420836},
issn = {1745-7270},
abstract = {Berberine (BBR) is used to treat diarrhea clinically. However, its reproductive toxicity is unclear. This study aims to investigate the impact of BBR on the male reproductive system. Intragastric BBR administration for 14 consecutive days results in a significant decrease in the serum testosterone concentration, epididymal sperm concentration, mating rate and fecundity of male mice. Testicular treatment with testosterone propionate (TP) partially reverses the damage caused by BBR to the male reproductive system. Mechanistically, the decrease in Muribaculaceae abundance in the gut microbiota of mice is the principal cause of the BBR-induced decrease in the sperm concentration. Both fecal microbiota transplantation (FMT) and polyethylene glycol (PEG) treatment demonstrate that Muribaculaceae is necessary for spermatogenesis. The intragastric administration of Muribaculaceae intestinale to BBR-treated mice restores the sperm concentration and testosterone levels. Metabolomic analysis reveals that BBR affects arginine and proline metabolism, of which ornithine level is downregulated. Combined analysis via 16S rRNA metagenomics sequencing and metabolomics shows that Muribaculaceae regulates ornithine level. The transcriptomic results of the testes indicate that the expressions of genes related to the low-density lipoprotein receptor (LDLR)-mediated testosterone synthesis pathway decrease after BBR administration. The transcriptional activity of the Ldlr gene in TM3 cells is increased with increased ornithine supplementation in the culture media, leading to increased testosterone synthesis. Overall, this study reveals an association between a BBR-induced decrease in Muribaculaceae abundance and defective spermatogenesis, providing a prospective therapeutic approach for addressing infertility-related decreases in serum testosterone triggered by changes in the gut microbiota composition.},
}
@article {pmid39420635,
year = {2024},
author = {Li, C and Sun, L and Jia, Z and Tang, Y and Liu, X and Zhang, J and Müller, C},
title = {Microbial Inoculants Drive Changes in Soil and Plant Microbiomes and Improve Plant Functions in Abandoned Mine Restoration.},
journal = {Plant, cell &amp; environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.15215},
pmid = {39420635},
issn = {1365-3040},
support = {//Jinchi Zhang acknowledges the funding support from Jiangsu Science and Technology Plan Project (BE2022420); the Innovation and Promotion of Forestry Science and Technology Program of Jiangsu Province (LYKJ[2021]30); the Scientific Research Project of Baishanzu National Park (2021ZDLY01); and the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD). Chong Li is grateful for the partial financial support from the Postgraduate Research and Practice Innovation Program of Jiangsu Province (KYCX21_0915), and the China Scholarship Council (202108320300)./ ; },
abstract = {The application of microbial inoculants holds promise for the sustainable restoration of abandoned mine sites by affecting soil nutrients and microbial communities. However, the responses of plant microbial communities to microbial inoculants in mine restoration remain largely unknown. To bridge this knowledge gap, we conducted a 4-year field experiment at an abandoned carbonate mine site to assess the impacts of microbial inoculants on the soil-plant microbiome. Our findings revealed that microbial inoculants significantly changed roots, fine root bacterial and fungal communities. Further, no significant correlations were observed between the soil-plant nutrient content (Z-score) and microbial alpha diversity. However, a significantly positive correlation was found between the relative abundance of the keystone ecological cluster (Module #1) and soil-plant nutrient content. The application of microbial inoculants also increased complexity, albeit decreased stability of plant microbiome networks, alongside a reduction in stochastic assembly. Conversely, they decreased the complexity but increased the stability of soil microbiome networks, accompanied by an increase in stochastic assembly. Notably, the number of specifically enriched microbiome functional traits of roots and root nodules under the microbial inoculant treatments surpassed that of the control. In summary, our findings underscored the potential of microbial inoculants to enhance soil-plant functionality at abandoned mine restoration sites.},
}
@article {pmid39420033,
year = {2024},
author = {Majzoub, ME and Paramsothy, S and Haifer, C and Parthasarathy, R and Borody, TJ and Leong, RW and Kamm, MA and Kaakoush, NO},
title = {The phageome of patients with ulcerative colitis treated with donor fecal microbiota reveals markers associated with disease remission.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {8979},
pmid = {39420033},
issn = {2041-1723},
support = {988415//Crohn&apos;s and Colitis Foundation (Crohn&apos;s &amp; Colitis Foundation)/ ; APP2011047//Department of Health | National Health and Medical Research Council (NHMRC)/ ; Investigator grant//Department of Health | National Health and Medical Research Council (NHMRC)/ ; Scientia fellowship//University of New South Wales (UNSW Australia)/ ; },
mesh = {Humans ; *Colitis, Ulcerative/therapy/microbiology/virology ; *Fecal Microbiota Transplantation ; *Bacteriophages/genetics/isolation &amp; purification/physiology ; *Gastrointestinal Microbiome/genetics ; *Feces/microbiology/virology ; Double-Blind Method ; Male ; Female ; Metagenomics/methods ; Adult ; Dysbiosis/microbiology/therapy ; Middle Aged ; Virome/genetics ; Remission Induction ; Anti-Bacterial Agents/therapeutic use ; Biomarkers ; },
abstract = {Bacteriophages are influential within the human gut microbiota, yet they remain understudied relative to bacteria. This is a limitation of studies on fecal microbiota transplantation (FMT) where bacteriophages likely influence outcome. Here, using metagenomics, we profile phage populations - the phageome - in individuals recruited into two double-blind randomized trials of FMT in ulcerative colitis. We leverage the trial designs to observe that phage populations behave similarly to bacterial populations, showing temporal stability in health, dysbiosis in active disease, modulation by antibiotic treatment and by FMT. We identify a donor bacteriophage putatively associated with disease remission, which on genomic analysis was found integrated in a bacterium classified to Oscillospiraceae, previously isolated from a centenarian and predicted to produce vitamin B complex except B12. Our study provides an in-depth assessment of phage populations during different states and suggests that bacteriophage tracking has utility in identifying determinants of disease activity and resolution.},
}
@article {pmid39419961,
year = {2024},
author = {Becsei, &#xc1; and Fuschi, A and Otani, S and Kant, R and Weinstein, I and Alba, P and Stéger, J and Visontai, D and Brinch, C and de Graaf, M and Schapendonk, CME and Battisti, A and De Cesare, A and Oliveri, C and Troja, F and Sironen, T and Vapalahti, O and Pasquali, F and Bányai, K and Makó, M and Pollner, P and Merlotti, A and Koopmans, M and Csabai, I and Remondini, D and Aarestrup, FM and Munk, P},
title = {Author Correction: Time-series sewage metagenomics distinguishes seasonal, human-derived and environmental microbial communities potentially allowing source-attributed surveillance.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {8953},
doi = {10.1038/s41467-024-53282-6},
pmid = {39419961},
issn = {2041-1723},
}
@article {pmid39419776,
year = {2024},
author = {Ma, M and Ardalan, A and Van Dyk, A and Charles, TC and Horsman, GP},
title = {Discovery of a Glyphosate Oxidase in Nature.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnae086},
pmid = {39419776},
issn = {1574-6968},
abstract = {Glyphosate is the most used herbicide on Earth. After a half-century of use we know only two biodegradative pathways, each of which appears to degrade glyphosate incidentally. One pathway begins with oxidation of glyphosate catalyzed by glycine oxidase (GO). To date, no naturally-occurring GO enzymes preferentially oxidize glyphosate but nonetheless are sufficiently active to initiate its degradation. However, GO enzymes that preferentially oxidize glyphosate over glycine - i.e. glyphosate oxidases - may have evolved in environments facing prolonged glyphosate exposure. To test this hypothesis, we screened a metagenomic library from glyphosate-exposed agricultural soil and identified a glyphosate oxidase from clone 11AW19 (GO19) that prefers glyphosate over glycine by four orders of magnitude. This is the first GO isolated from a natural source exhibiting a glyphosate preference. Not only have we discovered the first glyphosate oxidase in nature, but we have also demonstrated the utility of functional metagenomics to find a glyphosate oxidase with greater catalytic efficiency and specificity than those engineered using directed evolution.},
}
@article {pmid39419193,
year = {2024},
author = {Chen, H and Zeng, M and Batool, SS and Zhao, Y and Yu, Z and Zhou, J and Liu, K and Huang, J},
title = {Metagenomic analysis reveals effects of gut microbiome in response to neoadjuvant chemoradiotherapy in advanced rectal cancer.},
journal = {Genomics},
volume = {},
number = {},
pages = {110951},
doi = {10.1016/j.ygeno.2024.110951},
pmid = {39419193},
issn = {1089-8646},
abstract = {Neoadjuvant chemoradiotherapy can enhance survival rate of patients with advanced rectal cancer, but its effectiveness varies considerably. Previous studies have indicated that gut microbes may serve as biomarkers for predicting treatment efficacy. However, the specific roles of the gut microbiome in patients who have good response to nCRT remains unclear. In this study, shotgun metagenomic sequencing technology was used to analyze the fecal microbiome of patients with varying responses to nCRT. Our findings revealed that beneficial intestinal bacteria and genes from different metabolic pathways (carbohydrate metabolism, amino acid metabolism, and sulfur metabolism) were significantly enriched in patients with good response. Additionally, causal relationship in which microbial-derived GDP-D-rhamnose and butyrate could influence the response to nCRT was clarified. Our results offered new insights into the different response to nCRT, and provided valuable reference points for improving the effectiveness of nCRT in patients with advanced colorectal cancer.},
}
@article {pmid39418906,
year = {2024},
author = {Zhao, W and Ma, H and Gao, Z and Li, D and Lin, Y and Wu, C and Wei, L},
title = {Uncovering the toxic effects and adaptive mechanisms of aminated polystyrene nanoplastics on microbes in sludge anaerobic digestion system: Insight from extracellular to intracellular.},
journal = {Journal of hazardous materials},
volume = {480},
number = {},
pages = {136163},
doi = {10.1016/j.jhazmat.2024.136163},
pmid = {39418906},
issn = {1873-3336},
abstract = {The impacts of polystyrene nanoplastics (PS NPs) with amino functional groups on sludge anaerobic digestion process and the underlying microbial feedbacks remains unclear. Herein, PS NPs coated with and without amino functional groups were employed to explore their impacts on the sludge digestion performance. Experimental results showed that aminated PS NPs (PS-NH2) deteriorated the methane yield and hydrolysis rate. The Derjaguin-Landau-Verwey-Overbeek theory analysis suggested that the PS-NH2 decreased the interaction energy barrier, making it easier to contact with sludge and disrupting the structure of extracellular polymeric substances. Metagenomic analysis showed that the abundance of functional microbes (e.g., Longilinea, Leptolinea, and Methanosarcina) decreased, accompanied with lower network complexity and fewer keystone taxa. Molecular docking revealed that PS-NH2 occupy the antioxidant enzyme active binding sites through hydrogen bonding and hydrophobic interactions, impairing degradation of reactive oxygen species. The severe intracellular oxidative stress up-regulated genes associated with quorum sensing (e.g., luxI and luxR) and protein biosynthesis (e.g., algA, trpG and trpE), and further inducing compact tryptophan-like proteins as a defense against NPs. These findings provide new understanding of the toxic effects from PS-NH2 in biological systems and offer valuable insights into the regulation strategies aimed at alleviating NPs inhibition.},
}
@article {pmid39418853,
year = {2024},
author = {Aydin, F and Tarhane, S and Karakaya, E and Abay, S and Kayman, T and Güran, &#xd6; and Bozkurt, E and Üzüm, N and Avci, A and Olgun, K and Jablonski, D and Güran, C and Burçin Saticioğlu, &#x130;},
title = {Helicobacter cappadocius sp. nov., from lizards: The first psychrotrophic Helicobacter species.},
journal = {Systematic and applied microbiology},
volume = {47},
number = {6},
pages = {126557},
doi = {10.1016/j.syapm.2024.126557},
pmid = {39418853},
issn = {1618-0984},
abstract = {It was aimed to determine the prevalence of Helicobacter in some reptilian and amphibian species in Türkiye and to describe the bacteria. For this purpose, 73 cloacal swab samples were used as material. The description of the isolates was performed by detailed phenotypic tests, whole genome analyses, and MALDI-TOF MS. As a result of the phenotypic analysis, two helical, curved Gram-negative, motile isolates were recovered. It was determined through the analysis of 16S rRNA gene sequences that two isolates belonged to the genus Helicobacter. These isolates were found to be in a distinct group from other Helicobacter species. However, the 16S rRNA sequence did not match any identified species, with the closest match being Helicobacter mustelae strain R85-13-6[T], which had an identity level of 96.2 %. Additionally, it was found that strains faydin-H75[T] and faydin-H76 had a 99.3 % identity level for their 16S rRNA genes. After conducting dDDH and ANI analyses, it was found that strains faydin-H75[T] and their close neighbors H.anseris ATCC BAA-1299[T] shared 13.5 % and 68.8 % similarity, respectively. The genome size of the strains was 1.7 Mb while G + C contents were 33.5 %. Metagenomic analyses using IMNGS and Protologger tools revealed the presence of faydin-H75[T] in various lizard species with high similarity, confirming its broad distribution and host specificity. The results indicated that these two strains represent a novel species, for which we propose the name Helicobacter cappadocius with faydin-H75[T] (=NCTC014972 = LMG 33382 = DSM117062) as the respective type strain. The current novel species is the first Helicobacter species to exhibit a psychrotrophic feature.},
}
@article {pmid39418785,
year = {2024},
author = {Chen, J and Su, Z and Li, F and Cao, F and Xiong, F and Jiang, B and Xing, Y and Wen, D},
title = {The variation of resistome, mobilome and pathogen in domestic and industrial wastewater treatment systems.},
journal = {Environment international},
volume = {193},
number = {},
pages = {109051},
doi = {10.1016/j.envint.2024.109051},
pmid = {39418785},
issn = {1873-6750},
abstract = {Wastewater treatment plants (WWTPs), including both domestic and industrial facilities, are key contributors to antibiotic resistance genes (ARGs) and human pathogens in the environment. However, the characteristics and dissemination mechanisms of ARGs in domestic (SD) and industrial (SI) wastewater treatment systems remain unclear, leading to uncertainties in risk assessment. Based on metagenomic analysis, we observed significant differences in the compositions of resistome (ARGs and metal resistance genes, MRGs), mobilome (mobile genetic elements, MGEs), and bacterial community between SD and SI. SI exhibited lower diversity of ARGs but higher abundance of MRGs compared to SD. The removal efficiency of resistome was lower in the SI than that in the SD. MGEs emerged as the primary driver of ARG dissemination in the WWTPs, followed by the bacterial community. Environmental conditions (physicochemical parameters, heavy metals, and antibiotics) indirectly influenced the variation of resistome. Significantly, environmental conditions and MGEs highly influenced the composition of resistome in the SI, while bacterial community more associated with resistome in the SD. Additionally, we identified 36 human bacterial pathogens as potential hosts of ARGs, MRGs, and MGEs in wastewater samples. This study provides new insights on the dissemination mechanisms and risk assessment of antimicrobial resistance in the different types of WWTPs.},
}
@article {pmid39418776,
year = {2024},
author = {Xie, Q and Sun, J and Sun, M and Wang, Q and Wang, M},
title = {Perturbed microbial ecology in neuromyelitis optica spectrum disorder: Evidence from the gut microbiome and fecal metabolome.},
journal = {Multiple sclerosis and related disorders},
volume = {92},
number = {},
pages = {105936},
doi = {10.1016/j.msard.2024.105936},
pmid = {39418776},
issn = {2211-0356},
abstract = {BACKGROUND: Neuromyelitis optica spectrum disorder (NMOSD) is a central nervous system inflammatory demyelinating immune-mediated ailment, which is influenced by genetic, epigenetic, and environmental elements. The escalating incidence of NMOSD in recent years implies alterations in environmental risk factors. Recent research has established a correlation between gut microbiomes and the development of NMOSD.<br><br>METHODS: Metagenomic shotgun sequencing and gas chromatography-mass spectrometry (GC-MS) were employed to assess alterations of the structure and function in the fecal microbiome, as well as levels of short-chain fatty acids (SCFAs) in fecal and blood samples, among individuals with neuromyelitis optica spectrum disorder (NMOSD) during the acute phase (n = 25), the remission phase (n = 11), and a group of healthy controls (HCs) (n = 24). We further explored the correlation between gut microbiota and the pathogenesis of NMOSD through fecal microbiota transplantation (FMT). The gut microbiome from human donors diagnosed with NMOSD or HCs was transplanted into germ-free mice, followed by an analysis of the alterations in the structure and functionality of the transplanted mice's gut microbiome. Additionally, the impact of microbiome transfer on the immunity and spinal cord of germ-free mice was assessed through various techniques, including ELISA, flow cytometry, western blot, histopathology, and transcriptome sequencing.<br><br>RESULTS: (1) At the taxonomic levels of genus and species, there were significant differences in the &#x3b1;-diversity of the microbiome between HCs and NMOSD patients in the acute phase, with NMOSD patients having higher species diversity. (2) In the acute phase, the gut microbiota of NMOSD patients was characterized by Ruminococcaceae_unclassified, Campylobacter, Parabacteroides, Lactobacillus, Akkermansia, Streptococcus oralis, Clostridium leptum, Clostridium asparagiforme, Firmicutes bacterium CAG 238, and Lactobacillus fermentum. (3) The relative abundances of Coprobacter, Turicimonas, Gemmiger, Enterobacter, Roseburia sp.CAG 471, Veillonella tobetsuensis, Proteobacteria bacterium CAG 139, Ruminococcus bicirculans, Lactococcus lactis, Flavonifractor plautii, and Streptococcus cristatus were notably lower in patients experiencing remission compared to NMOSD patients in the acute phase, On the other hand, the relative abundances of Flavonifractor (P = 0.049) and Clostridium aldenense (P = 0.049) were significantly higher. Following medication, the gut microbiome distribution in NMOSD patients during remission closely resembled that of healthy controls (HCs). (4) Compared with HCs, acetate levels in the feces of patients with NMOSD in the acute phase were significantly lower. (5) In addition, we transplanted feces from NMOSD patients into germ-free mice and revealed a significant increase in the levels of IL-6, IL-17A, and IL-23 in the blood of mice belonging to the NMOSD fecal transplantation (NFMT) group. Additionally, the IL-10 level exhibited a significant reduction. Moreover, the proportion of Th17 cells displayed a significant increase, while the proportion of Treg cells exhibited a significant decrease in the spleens of NFMT mice.<br><br>CONCLUSION: Patients in the acute phase of neuromyelitis optica spectrum disorder (NMOSD) exhibited imbalances in their gut microbiota and a deficiency in short-chain fatty acids (SCFAs). Following drug treatment, the composition of intestinal microbes in NMOSD patients during the remission phase closely resembled that of the healthy control population. The FMT experiment provided evidence of the significant association between intestinal flora and the pathogenesis of NMOSD. Consequently, investigating gut microbiota and identifying novel microbial markers hold promise for the diagnosis and treatment of NMOSD patients.},
}
@article {pmid39418385,
year = {2024},
author = {Lien, YW and Amendola, D and Lee, KS and Bartlau, N and Xu, J and Furusawa, G and Polz, MF and Stocker, R and Weiss, GL and Pilhofer, M},
title = {Mechanism of bacterial predation via ixotrophy.},
journal = {Science (New York, N.Y.)},
volume = {386},
number = {6719},
pages = {eadp0614},
doi = {10.1126/science.adp0614},
pmid = {39418385},
issn = {1095-9203},
mesh = {*Cryoelectron Microscopy ; Type VI Secretion Systems/metabolism/genetics ; Single-Cell Analysis ; Bacteria/metabolism/genetics ; },
abstract = {Ixotrophy is a contact-dependent predatory strategy of filamentous bacteria in aquatic environments for which the molecular mechanism remains unknown. We show that predator-prey contact can be established by gliding motility or extracellular assemblages we call "grappling hooks." Cryo-electron microscopy identified the grappling hooks as heptamers of a type IX secretion system substrate. After close predator-prey contact is established, cryo-electron tomography and functional assays showed that puncturing by a type VI secretion system mediated killing. Single-cell analyses with stable isotope-labeled prey revealed that prey components are taken up by the attacker. Depending on nutrient availability, insertion sequence elements toggle the activity of ixotrophy. A marine metagenomic time series shows coupled dynamics of ixotrophic bacteria and prey. We found that the mechanism of ixotrophy involves multiple cellular machineries, is conserved, and may shape microbial populations in the environment.},
}
@article {pmid39418300,
year = {2024},
author = {Zhang, Y and Mao, M and Zhang, R and Liao, YT and Wu, VCH},
title = {DeepPL: A deep-learning-based tool for the prediction of bacteriophage lifecycle.},
journal = {PLoS computational biology},
volume = {20},
number = {10},
pages = {e1012525},
doi = {10.1371/journal.pcbi.1012525},
pmid = {39418300},
issn = {1553-7358},
abstract = {Bacteriophages (phages) are viruses that infect bacteria and can be classified into two different lifecycles. Virulent phages (or lytic phages) have a lytic cycle that can lyse the bacteria host after their infection. Temperate phages (or lysogenic phages) can integrate their phage genomes into bacterial chromosomes and replicate with bacterial hosts via the lysogenic cycle. Identifying phage lifecycles is a crucial step in developing suitable applications for phages. Compared to the complicated traditional biological experiments, several tools have been designed for predicting phage lifecycle using different algorithms, such as random forest (RF), linear support-vector classifier (SVC), and convolutional neural network (CNN). In this study, we developed a natural language processing (NLP)-based tool-DeepPL-for predicting phage lifecycles via nucleotide sequences. The test results showed that our DeepPL had an accuracy of 94.65% with a sensitivity of 92.24% and a specificity of 95.91%. Moreover, DeepPL had 100% accuracy in lifecycle prediction on the phages we isolated and biologically verified previously in the lab. Additionally, a mock phage community metagenomic dataset was used to test the potential usage of DeepPL in viral metagenomic research. DeepPL displayed a 100% accuracy for individual phage complete genomes and high accuracies ranging from 71.14% to 100% on phage contigs produced by various next-generation sequencing technologies. Overall, our study indicates that DeepPL has a reliable performance on phage lifecycle prediction using the most fundamental nucleotide sequences and can be applied to future phage and metagenomic research.},
}
@article {pmid39418241,
year = {2024},
author = {Song, C and Liu, F and Mei, Y and Cai, W and Cheng, K and Guo, D and Liu, Y and Shi, H and Duan, DD and Liu, Z},
title = {Integrated metagenomic and metabonomic mechanisms for the therapeutic effects of Duhuo Jisheng decoction on intervertebral disc degeneration.},
journal = {PloS one},
volume = {19},
number = {10},
pages = {e0310014},
doi = {10.1371/journal.pone.0310014},
pmid = {39418241},
issn = {1932-6203},
mesh = {Animals ; *Intervertebral Disc Degeneration/drug therapy/metabolism/microbiology ; *Drugs, Chinese Herbal/pharmacology/therapeutic use ; *Metabolomics/methods ; Rats ; *Gastrointestinal Microbiome/drug effects ; Male ; *Rats, Sprague-Dawley ; *Metagenomics/methods ; Metabolome/drug effects ; Feces/microbiology ; Disease Models, Animal ; },
abstract = {Intervertebral disc degeneration (IVDD) is a prevalent orthopedic condition with lower back pain as the predominant clinical presentation that challenges clinical treatment with few therapeutic options. Duhuo Jisheng Decoction (DHJSD) has been proven effective in the therapy of IVDD, but the precise underlying mechanisms remain not fully elucidated. The current study was designed to test our hypothesis that DHJSD may systematically correct the phenotypic disruption of the gut microbiota and changes in the serum metabolome linked to IVDD. Analysis of the active ingredients of DHJSD by ultra high performance liquid chromatography. An integrated metagenomic and metabonomic approach was used to analyze feces and blood samples from normal and IVDD rats. Compared to the control group, fiber ring pinning on the caudal 3 to caudal 5 segments of the rats caused IVDD and significantly altered the compositions of the intestinal microbiota and serum metabolites. Integrated analysis revealed commonly-altered metabolic pathways shared by both intestinal microbiota and serum metabolome of the IVDD rats. DHJSD inhibited the degenerative process and restored the compositions of the perturbed gut microbiota, particularly the relative abundance of commensal microbes of the Prevotellaceae family. DHJSD also corrected the altered metabolic pathways involved in the metabolism of glycine, serine, threonine, valine, the citric acid cycle, and biosynthesis of leucine and isoleucine. DHJSD inhibited the disc degeneration process by an integrated metagenomic and metabonomic mechanism to restore the microbiome profile and normalize the metabonomic pathways.},
}
@article {pmid39417646,
year = {2024},
author = {Wang, Q and Geng, L and Gao, Z and Sun, Y and Li, X and Sun, S and Luo, Y},
title = {Microalgae Enhances the Adaptability of Epiphytic Bacteria to Sulfamethoxazole Stress and Proliferation of Antibiotic Resistance Genes Mediated by Integron.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c04925},
pmid = {39417646},
issn = {1520-5851},
abstract = {The transmission of ARGs in the microalgae-associated epiphytic bacteria remains unclear under antibiotic exposure, apart from altering the microbial community structure. In this study, Chlorella vulgaris cocultured with bacteria screened from surface water was examined to explore the spread of ARGs in the presence of sulfamethoxazole (SMX). The extracellular polymers released by Chlorella vulgaris could reduce antibiotic-induced collateral damage to bacteria, thus increasing the diversity of the microalgae-associated epiphytic bacteria. The abundances of sul1 and intI1 in the phycosphere at 1 mg/L SMX dose increased by 290 and 28 times, respectively. Metagenomic sequencing further confirmed that SMX bioaccumulation stimulated the horizontal transfer of sul1 mediated by intI1 in the microalgae-associated epiphytic bacteria, while reactive oxygen species (ROS)-mediated oxidative stress induced the SOS response and thus enhanced the transformation of sul1 in the J group. This is the first study to verify that microalgae protect bacteria from antibiotic damage and hinder the spread of ARGs mediated by SOS response, while the transfer of ARGs mediated by integron is promoted due to the bioaccumulation of SMX in the phycosphere. The results contribute to present comprehensive understanding of the risk of ARG proliferation by the presence of emerging contaminants residues in river.},
}
@article {pmid39417540,
year = {2024},
author = {Ginatt, AA and Berihu, M and Castel, E and Medina, S and Carmi, G and Faigenboim-Doron, A and Sharon, I and Tal, O and Droby, S and Somera, T and Mazzola, M and Eizenberg, H and Freilich, S},
title = {A metabolic modeling-based framework for predicting trophic dependencies in native rhizobiomes of crop plants.},
journal = {eLife},
volume = {13},
number = {},
pages = {},
doi = {10.7554/eLife.94558},
pmid = {39417540},
issn = {2050-084X},
support = {US-5390-21//United States-Israel Binational Agricultural Research and Development Fund/ ; },
mesh = {*Rhizosphere ; *Malus/microbiology/metabolism ; *Microbiota ; Plant Roots/microbiology/metabolism ; Soil Microbiology ; Bacteria/metabolism/genetics/classification ; Crops, Agricultural/microbiology ; Metabolomics/methods ; Models, Biological ; },
abstract = {The exchange of metabolites (i.e., metabolic interactions) between bacteria in the rhizosphere determines various plant-associated functions. Systematically understanding the metabolic interactions in the rhizosphere, as well as in other types of microbial communities, would open the door to the optimization of specific predefined functions of interest, and therefore to the harnessing of the functionality of various types of microbiomes. However, mechanistic knowledge regarding the gathering and interpretation of these interactions is limited. Here, we present a framework utilizing genomics and constraint-based modeling approaches, aiming to interpret the hierarchical trophic interactions in the soil environment. 243 genome scale metabolic models of bacteria associated with a specific disease-suppressive vs disease-conducive apple rhizospheres were drafted based on genome-resolved metagenomes, comprising an in silico native microbial community. Iteratively simulating microbial community members' growth in a metabolomics-based apple root-like environment produced novel data on potential trophic successions, used to form a network of communal trophic dependencies. Network-based analyses have characterized interactions associated with beneficial vs non-beneficial microbiome functioning, pinpointing specific compounds and microbial species as potential disease supporting and suppressing agents. This framework provides a means for capturing trophic interactions and formulating a range of testable hypotheses regarding the metabolic capabilities of microbial communities within their natural environment. Essentially, it can be applied to different environments and biological landscapes, elucidating the conditions for the targeted manipulation of various microbiomes, and the execution of countless predefined functions.},
}
@article {pmid39417505,
year = {2024},
author = {Kanehisa, M and Furumichi, M and Sato, Y and Matsuura, Y and Ishiguro-Watanabe, M},
title = {KEGG: biological systems database as a model of the real world.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkae909},
pmid = {39417505},
issn = {1362-4962},
support = {JPMJND2203//NBDC Database Integration Coordination Program/ ; //Japan Science and Technology Agency/ ; },
abstract = {KEGG (https://www.kegg.jp/) is a database resource for representation and analysis of biological systems. Pathway maps are the primary dataset in KEGG representing systemic functions of the cell and the organism in terms of molecular interaction and reaction networks. The KEGG Orthology (KO) system is a mechanism for linking genes and proteins to pathway maps and other molecular networks. Each KO is a generic gene identifier and each pathway map is created as a network of KO nodes. This architecture enables KEGG pathway mapping to uncover systemic features from KO assigned genomes and metagenomes. Additional roles of KOs include characterization of conserved genes and conserved units of genes in organism groups, which can be done by taxonomy mapping. A new tool has been developed for identifying conserved gene orders in chromosomes, in which gene orders are treated as sequences of KOs. Furthermore, a new dataset called VOG (virus ortholog group) is computationally generated from virus proteins and expanded to proteins of cellular organisms, allowing gene orders to be compared as VOG sequences as well. Together with these datasets and analysis tools, new types of pathway maps are being developed to present a global view of biological processes involving multiple organism groups.},
}
@article {pmid39417302,
year = {2024},
author = {Li, J and Fang, W and Li, C and Cui, M and Qian, L and Jiang, Z and Jiang, Y and Shi, L and Xie, X and Guo, H and Li, P and Dong, Y and Xiu, W and Wang, Y and Wang, Y},
title = {Dissimilatory Iodate-Reducing Microorganisms Contribute to the Enrichment of Iodine in Groundwater.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c04455},
pmid = {39417302},
issn = {1520-5851},
abstract = {Iodate reduction by dissimilatory iodate-reducing microorganisms (DIRMs) plays a crucial role in the biogeochemical cycling of iodine on Earth. However, the occurrence and distribution of DIRMs in iodine-rich groundwater remain unclear. In this study, we isolated the dissimilatory iodate-reducing bacteriumAzonexus hydrophilusstrain NCP973 from a geogenic high-iodine groundwater of China for the first time. The analysis of genome, transcriptome, and heterologous expression revealed that strain NCP973 uses the dissimilatory iodate-reducing enzyme IdrABP1P2 to reduce dissolved or in situ sediment-bound iodate to iodide. The location of IdrABP1P2 in the conjugative plasmid of strain NCP973 implies that IdrABP1P2 could be spread by horizontal gene transfer and allow the recipient microorganisms to participate in the enrichment of iodide in aquifers. Based on the global iodine-rich groundwater metagenomes and genomes, the identification of idrA showed that phylogenetically diverse DIRMs are widely distributed not only in geogenic high-iodine groundwater of China but also in radionuclide-contaminated groundwater of USA as well as in subsurface cavern waters in Germany and Italy. Moreover, the abundance of idrA was found to be higher in groundwater with a relatively high iodine content. Collectively, these results suggest that terrestrial iodine-affected groundwater systems are another important habitat for DIRMs in addition to marine environments, and their activity in aquifers triggers the mobilization and enrichment of iodine in groundwater worldwide.},
}
@article {pmid39417122,
year = {2024},
author = {Atugonza, C and Muwonge, A and Najjuka, CF and Kateete, DP and Katagirya, E and Mwesigwa, S and Asiimwe, B},
title = {Early changes in the gut microbiome among HIV-infected Individuals in Uganda initiating daily TMP/SMX.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.10.07.24315002},
pmid = {39417122},
abstract = {Daily cotrimoxazole (TMP/SXT) prophylaxis is part of the HIV treatment package for all new HIV-infected individuals in Uganda. Although this treatment has shown reduced morbidity and mortality in HIV, it remains controversial due to its contribution to developing antibiotic-resistant bacteria. Moreover, the effects of daily use of a broad-spectrum antibiotic on the gut microbiome remain unknown. To study the early effects, we analysed shotgun metagenome sequence data from stool samples of five newly HIV-infected individuals initiating TMP/SXT prophylaxis longitudinally for the first 30 days of treatment. Using shotgun metagenomics sequencing, we generated both taxonomic and functional profiles from each patient and compared gut microbial changes Pre-TMP/SXT and post-TMP/SXT on Day 5, Day 14, and Day 30. Daily TMP/SXT prophylaxis resulted in a shift characterised by an enrichment of Prevetollea and Ruminococcus genera members and the depletion of Lactococcus and Bacteroides genera members. Furthermore, these microbial shifts were associated with changes in the functional profile revealed by a differential abundance of pathways of amino acid metabolism, carbohydrate metabolism, and nucleotide biosynthesis linked to members of the Bacteroidaceae and Enterobacteriaceae families. TMP/SXT daily prophylaxis in HIV-infected individuals is associated with dramatic changes in microbial composition and functional profiles; however, other factors such as Age, Gender, HIV clinical stage, and ART regiment are at play. Further investigation is needed to examine the implication of these shifts on clinical management and outcomes among HIV patients.},
}
@article {pmid39417080,
year = {2024},
author = {You, R and Yu, Y and Shen, M and Zhang, Y and Hong, J and Kang, Y},
title = {Applications of different forms of nitrogen fertilizers affect soil bacterial community but not core ARGs profile.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1447782},
doi = {10.3389/fmicb.2024.1447782},
pmid = {39417080},
issn = {1664-302X},
abstract = {The objective of this study was to investigate the impact of various chemical nitrogen fertilizers on the profile of antibiotic resistance genes (ARGs) in soil. A microcosm experiment was conducted with four treatments, including CK (control with no nitrogen), AN (ammonium nitrogen), NN (nitrate nitrogen), and ON (urea nitrogen), and the abundance of ARGs was assessed over a 30-day period using a metagenomic sequencing approach. The levels of core ARGs varied between 0.16 and 0.22 copies per cell across different treatments over time. The abundance of core ARGs in the ON treatment closely resembled that of the CK treatment, suggesting that environmentally friendly nitrogen fertilizers, particularly those in controlled release formulations, may be preferable. The core ARG abundance in the AN and NN treatments exhibited noticeable fluctuations over time. Overall, chemical nitrogen fertilizers had minimal effects on the core ARG profile as determined by principal component analysis and clustering analyses. Conversely, distinct and significant changes in bacterial communities were observed with the use of different nitrogen fertilizers. However, the influence of nitrogen fertilizers on the core ARGs is limited due to the unaffected potential bacterial hosts. Nitrogen-cycling-related genes (NCRGs), such as those involved in nitrogen-fixing (nifK, nifD, nifH) and denitrification (narG, napA, nirK, norB, nosZ) processes, exhibit a positive correlation with ARGs (rosA, mexF, bacA, vanS), indicating a potential risk of ARG proliferation during intense denitrification activities. This study indicates that the application of chemical nitrogen has a minimal effect on the abundance of ARGs in soil, thereby alleviating concerns regarding the potential accumulation of ARGs due to the use of chemical nitrogen fertilizers.},
}
@article {pmid39416816,
year = {2024},
author = {Shamim, U and Yadav, A and Maurya, R and Devi, P and Kumari, P and Kanika, and Khare, K and Tarai, B and Pandey, R},
title = {Functional metagenomics highlights varied infection states with dynamics of pathogens and antibiotic resistance in lower respiratory tract infections.},
journal = {Heliyon},
volume = {10},
number = {19},
pages = {e38380},
doi = {10.1016/j.heliyon.2024.e38380},
pmid = {39416816},
issn = {2405-8440},
abstract = {BACKGROUND: Antimicrobial resistance (AMR) amongst pathogenic bacterial species poses significant challenges in treating infections of the lower respiratory tract (LRT), leading to higher hospitalization and mortality rates.<br><br>METHODS: Bronchoalveolar lavage fluid (BALF) from 84 clinically adjudicated LRTI patients were subjected to respiratory pathogen ID/AMR (RPIP) enrichment and sequencing followed by Explify and CZID seq data analysis to identify potential LRTI pathogens and associated AMR genes. Patients were categorized as LRTI-WP (with pneumonia) and LRTI-WoP (without pneumonia).<br><br>FINDINGS: mNGS achieved 100&#xa0;% pathogen detection compared to 73&#xa0;% through clinician-used BioFire panel. Predominant pathogens included Acinetobacter baumannii, Klebsiella pneumoniae along with detection of Aspergillus versicolor and Herpes simplex virus. Double and polymicrobial infections were captured, involving non-respiratory pathogens like Rothia mucilaginosa, Escherichia coli, and Moraxella osloensis. AMR detection highlighted macrolide (MPH; ERM) and Sulfonamide (SUL) rich resistome in 60&#xa0;% of patients followed by extended spectrum beta lactamase (OXA) and tetracycline (TET). LRTI-WP showed high abundance of A. baumannii, majorly associated with MPH whereas K. pneumoniae with beta-lactams was comparable in both groups. Differences in clinical severity may stem from non-respiratory pathogens, newly recognized via mNGS. CZID seq pipeline validated and revealed additional microbes and AMR genes in the cohort.<br><br>INTERPRETATION: The prevalence of common pathogens like A. baumannii and K. pneumoniae along with the non-respiratory pathogens identified by RPIP-Explify and CZID seq provided an understanding to evaluate the LRTI. mNGS is crucial for precise pathogen and antibiotic resistance detection, vital for combating antibiotic resistance.},
}
@article {pmid39416140,
year = {2024},
author = {Majernik, SN and Beaver, L and Bradley, PH},
title = {Small amounts of misassembly can have disproportionate effects on pangenome-based metagenomic analyses.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.10.11.617902},
pmid = {39416140},
issn = {2692-8205},
abstract = {Individual genes from microbiomes can drive host-level phenotypes. To help identify such candidate genes, several recent tools estimate microbial gene copy numbers directly from metagenomes. These tools rely on alignments to pangenomes, which in turn are derived from the set of all individual genomes from one species. While large-scale metagenomic assembly efforts have made pangenome estimates more complete, mixed communities can also introduce contamination into assemblies, and it is unknown how robust pangenome-based metagenomic analyses are to these errors. To gain insight into this problem, we re-analyzed a case-control study of the gut microbiome in cirrhosis, focusing on commensal Clostridia previously implicated in this disease. We tested for differentially prevalent genes in the Lachnospiraceae , then investigated which were likely to be contaminants using sequence similarity searches. Out of 86 differentially prevalent genes, we found that 33 (38%) were probably contaminants originating in taxa such as Veillonella and Haemophilus , unrelated genera that were independently correlated with disease status. Our results demonstrate that even small amounts of contamination in metagenome assemblies, below typical quality thresholds, can threaten to overwhelm gene-level metagenomic analyses. However, we also show that such contaminants can be accurately identified using a method based on gene-to-species correlation. After removing these contaminants, we observe that several flagellar motility gene clusters in the Lachnospira eligens pangenome are associated with cirrhosis status. We have integrated our analyses into an analysis and visualization pipeline, PanSweep, that can automatically identify cases where pangenome contamination may bias the results of gene-resolved analyses.},
}
@article {pmid39416120,
year = {2024},
author = {Richardson, M and Zhao, S and Sheth, RU and Lin, L and Qu, Y and Lee, J and Moody, T and Ricaurte, D and Huang, Y and Velez-Cortes, F and Urtecho, G and Wang, HH},
title = {SAMPL-seq reveals micron-scale spatial hubs in the human gut microbiome.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.10.08.617108},
pmid = {39416120},
issn = {2692-8205},
abstract = {UNLABELLED: The local arrangement of microbes can profoundly impact community assembly, function, and stability. To date, little is known about the spatial organization of the human gut microbiome. Here, we describe a high-throughput and streamlined method, dubbed SAMPL-seq, that samples microbial composition of micron-scale sub-communities with split-and-pool barcoding to capture spatial colocalization in a complex consortium. SAMPL-seq analysis of the gut microbiome of healthy humans identified bacterial taxa pairs that consistently co-occurred both over time and across multiple individuals. These colocalized microbes organize into spatially distinct groups or "spatial hubs" dominated by Bacteroideceae , Ruminococceae , and Lachnospiraceae families. From a dietary perturbation using inulin, we observed reversible spatial rearrangement of the gut microbiome, where specific taxa form new local partnerships. Spatial metagenomics using SAMPL-seq can unlock new insights to improve the study of microbial communities.<br><br>ONE SENTENCE SUMMARY: High throughput micron-scale subcommunity sampling and sequencing identifies distinct spatial associations of gut bacteria within and across individuals.},
}
@article {pmid39416080,
year = {2024},
author = {Wang, Q and Wang, BY and Williams, S and Xie, H},
title = {Diversity and characteristics of the oral microbiome influenced by race and ethnicity.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.10.07.617037},
pmid = {39416080},
issn = {2692-8205},
abstract = {UNLABELLED: Periodontitis disproportionately affects racial/ethnic populations. Besides social determinants contributing to disparities in periodontal health, variations of oral microbial communities may also be a key factor influencing oral immune responses. To characterize the oral microbiome from different racial/ethnic populations, we collected 161 dental plaque samples from African Americans (AAs), Caucasian Americans (CAs), and Hispanic Americans (HAs) with clinical gingival health or biofilm-induced gingivitis on an intact periodontium. Using metagenomic sequencing, we found significant difference in diversity and abundance of microbial taxa in the dental plaque samples from AA, CA, and HA groups and unique microbial species that can only be detected in a particular racial/ethnic group. Moreover, we revealed racial/ethnic associated variations in functional potential of the oral microbiome, showing that diversity and abundance of antibiotic resistant genes were greater in the oral microbiome of the AAs than those in CAs or HAs, and that the AAs exhibited higher levels of genes involving in modification of glycoconjugates, oligo- and polysaccharides. These findings indicate more complex and higher virulence potential oral microbiome in AA and HA populations, which likely contributes to higher prevalence of periodontitis in AAs and HAs.<br><br>IMPORTANCE: Recognizing the variations in the oral microbiome among racial/ethnic populations offers insight into the microbial determinants contributing to oral health disparities. In the study presented here, we found a higher level of bleeding on probing (BOP), an indicator of tissue inflammatory response, in the AA group, which is correspondence with a more complex oral microbiome detected in this group. Our observations suggest that the variations of the oral microbiome associated with racial/ethnic backgrounds may directly relate to their virulence potential including their abilities to induce host immune responses and to resist antibiotic treatment. Therefore, these finding can be a stepping stone for developing precision medicine and personalized periodontal prevention/treatment and for reducing oral health disparities.},
}
@article {pmid39416003,
year = {2024},
author = {Jacoby, C and Scorza, K and Ecker, L and McMillin, M and Ramaswamy, R and Sundararajan, A and Sidebottom, AM and Lin, H and Dufault-Thompson, K and Hall, B and Jiang, X and Light, SH},
title = {Gut Bacteria Metabolize Natural and Synthetic Steroid Hormones via the Reductive OsrABC Pathway.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.10.08.617280},
pmid = {39416003},
issn = {2692-8205},
abstract = {Steroid hormone metabolism by the gut microbiome has multiple implications for mammalian physiology, but the underlying mechanisms and broader significance of this activity remains largely unknown. Here, we isolate a novel human gut bacterium, Clostridium steroidoreducens [T] strain HCS.1, that reduces cortisol, progesterone, testosterone, and related steroid hormones to 3β,5β-tetrahydrosteroid products. Through transcriptomics and heterologous enzyme profiling, we identify and biochemically characterize the C. steroidoreducens OsrABC reductive steroid hormone pathway. OsrA is a 3-oxo-Δ [1] -steroid hormone reductase that selectively targets the Δ [1] -bond present in synthetic steroid hormones, including the anti-inflammatory corticosteroids prednisolone and dexamethasone. OsrB is a promiscuous 3-oxo-Δ [4] -steroid hormone reductase that converts steroid hormones to 5β-dihydrosteroid intermediates. OsrC is a 3-oxo-5β-steroid hormone oxidoreductase that reduces 5β-intermediates to 3β,5β-tetrahydro products. We find that osrA and osrB homologs predict steroid hormone reductase activity in diverse gut bacteria and are enriched in Crohn's disease fecal metagenomes. These studies thus identify the basis of reductive steroid hormone metabolism in the gut and establish a link between inflammatory disease and microbial enzymes that deplete anti-inflammatory corticosteroids.},
}
@article {pmid39415203,
year = {2024},
author = {Tong, X and Luo, D and Leung, MHY and Lee, JYY and Shen, Z and Jiang, W and Mason, CE and Lee, PKH},
title = {Diverse and specialized metabolic capabilities of microbes in oligotrophic built environments.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {198},
pmid = {39415203},
issn = {2049-2618},
support = {BK20230230//Jiangsu Science and Technology Programme/ ; 11214721//Hong Kong Research Grants Council, General Research Fund/ ; R1016-20F//Hong Kong Research Grants Council, Research Impact Fund/ ; },
mesh = {Humans ; Hong Kong ; *Microbiota ; *Built Environment ; *Metagenome ; *Phylogeny ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Skin/microbiology ; Micrococcus luteus/genetics/metabolism ; Genome, Bacterial ; },
abstract = {BACKGROUND: Built environments (BEs) are typically considered to be oligotrophic and harsh environments for microbial communities under normal, non-damp conditions. However, the metabolic functions of microbial inhabitants in BEs remain poorly understood. This study aimed to shed light on the functional capabilities of microbes in BEs by analyzing 860 representative metagenome-assembled genomes (rMAGs) reconstructed from 738 samples collected from BEs across the city of Hong Kong and from the skin surfaces of human occupants. The study specifically focused on the metabolic functions of rMAGs that are either phylogenetically novel or prevalent in BEs.<br><br>RESULTS: The diversity and composition of BE microbiomes were primarily shaped by the sample type, with Micrococcus luteus and Cutibacterium acnes being prevalent. The metabolic functions of rMAGs varied significantly based on taxonomy, even at the strain level. A novel strain affiliated with the Candidatus class Xenobia in the Candidatus phylum Eremiobacterota and two novel strains affiliated with the superphylum Patescibacteria exhibited unique functions compared with their close relatives, potentially aiding their survival in BEs and on human skins. The novel strains in the class Xenobia possessed genes for transporting nitrate and nitrite as nitrogen sources and nitrosative stress mitigation induced by nitric oxide during denitrification. The two novel Patescibacteria strains both possessed a broad array of genes for amino acid and trace element transport, while one of them carried genes for carotenoid and ubiquinone biosynthesis. The globally prevalent M. luteus in BEs displayed a large and open pangenome, with high infraspecific genomic diversity contributed by 11 conspecific strains recovered from BEs in a single geographic region. The versatile metabolic functions encoded in the large accessory genomes of M. luteus may contribute to its global ubiquity and specialization in BEs.<br><br>CONCLUSIONS: This study illustrates that the microbial inhabitants of BEs possess metabolic potentials that enable them to tolerate and counter different biotic and abiotic conditions. Additionally, these microbes can efficiently utilize various limited residual resources from occupant activities, potentially enhancing their survival and persistence within BEs. A better understanding of the metabolic functions of BE microbes will ultimately facilitate the development of strategies to create a healthy indoor microbiome. Video Abstract.},
}
@article {pmid39414630,
year = {2024},
author = {Córdoba-Agudelo, M and Arboleda-Rivera, JC and Borrego-Muñoz, DA and Ramírez-Cuartas, CA and Pérez-Jaramillo, JE},
title = {Key Chemical Soil Parameters for the Assembly of Rhizosphere Bacteria Associated with Avocado Cv Hass Grafted on Landrace Rootstocks.},
journal = {Current microbiology},
volume = {81},
number = {12},
pages = {412},
pmid = {39414630},
issn = {1432-0991},
mesh = {*Persea/microbiology ; *Rhizosphere ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; *Soil/chemistry ; *Microbiota ; *RNA, Ribosomal, 16S/genetics ; *Plant Roots/microbiology ; Colombia ; Phylogeny ; },
abstract = {Avocado cultivation holds significant economic importance in many countries, ranking Colombia as the fifth largest global producer. Particularly, the Hass cultivar plays a pivotal role in Colombia's avocado industry, especially in the Department of Antioquia, the primary export region. This cultivar is grown under diverse soil and climate conditions and exhibits considerable genetic polymorphism due to the hybridization of varieties of agronomic significance, leading to a diverse array of landrace rootstocks. However, the role of soil conditions and rootstock genotype in structuring rhizosphere bacterial communities is still lacking. In addressing this knowledge gap, we investigated the influence of two soil conditions on the structure of rhizosphere bacterial communities associated with two landrace genotypes of Persea americana cv. Hass, utilizing 16S rRNA sequencing. Notably, no significant differences related to genotypes were observed. This study reports that the rhizosphere bacterial microbiome remains consistent across avocado landrace rootstocks, while variations in key parameters such as phosphorus, pH, Mg, and Ca drive distinct rhizosphere effects. Our results reveal that despite the soils having similar management, increases in these crucial parameters can lead to bacterial communities with lower alpha diversity and a more complex co-occurrence network. In addition, we found substantial variations in beta diversity, bacterial composition, and metagenome predictions between the two farms, underscoring the role of soil variables in shaping the bacterial microbiome. These findings provide valuable insights into the factors influencing the bacterial communities that may play a role in the health and productivity of crops with agro-industrial potential, such as Hass avocado.},
}
@article {pmid39414169,
year = {2024},
author = {Zhang, B and Zhang, N and Sui, H and Xue, R and Qiao, S},
title = {Unique ecology of biofilms and flocs: Bacterial composition, assembly, interaction, and nitrogen metabolism within deteriorated bioreactor inoculated with mature partial nitrification-anammox sludge.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {131643},
doi = {10.1016/j.biortech.2024.131643},
pmid = {39414169},
issn = {1873-2976},
abstract = {This work unraveled discrepant ecological patterns between biofilms and flocs in a deteriorated bioreactor inoculated with mature partial nitrification-anammox (PN/A) sludge. Based on 16S rRNA analysis, a comprehensive evaluation of neutral and null models, along with niche width, delineated that the bacterial community assembly in biofilms and flocs was dominantly driven by the stochastic process, and dispersal limitation critically shaped the community assembly. Co-occurrence network analysis revealed that environmental stress caused decentralized and fragmented bacterial colonies, and anammox bacteria were mainly peripheral in biofilms network and less involved in interspecific interactions. Simultaneous PN/A and partial denitrification-anammox (PD/A) processes were identified, whereas PN and PD process primarily occurred in the biofilms and flocs, respectively, as evidenced by metagenomics. Collectively, these outcomes are expected to deepen the basic understanding of complex microbial community and nitrogen metabolism under environmental disturbance, thereby better characterizing and serving the artificial ecosystems.},
}
@article {pmid39414063,
year = {2024},
author = {Yu, Y and Li, Y and Sun, B and Cui, J and Liu, H and Sun, Y and Xu, Q and Boisse, N and Voelker, F and Matioszek, D and Fvero, C and Kieffer, J and Li, Y and Lu, J and Li, H and Bao, M},
title = {Characterization and Degradation Mechanism of a Newly Isolated Hydrolyzed Polyacrylamide-degrading Bacterium Alcaligenes faecalis EPDB-5 from the Oilfield Sludge.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {125124},
doi = {10.1016/j.envpol.2024.125124},
pmid = {39414063},
issn = {1873-6424},
abstract = {Hydrolyzed polyacrylamide (HPAM) is posing serious threats to ecosystems. However, biodegradation is an effective method to remove HPAM owing to its low cost and environmental friendliness. In this study, Alcaligenes faecalis EPDB-5 was isolated as a highly efficient HPAM degrading strain from sludge contaminated with polymerized produced water from Daqing oilfield. Under the optimal conditions, the strain EPDB-5 demonstrated an impressive HPAM degradation rate of 86.05%, the total nitrogen (TN) removal of 71.96% and chemical oxygen demand (COD) removal of 67.98%. Meanwhile, it can maintain a stable degradation rate higher than 75% under different pH and temperature conditions. 27 genes that play a key role in HPAM degradation were annotated by metagenomics sequencing. The key genes were involved in multiple KEGG pathways, including biofilm formation, biosynthesis secondary metabolites, and metabolic pathways. SEM, GPC, and FTIR analyses revealed that the structure of HPAM after biodegradation showed pores, a significant decrease in molecular weight, -NH2 detachment, and carbon chain breakage. Particularly, we propose a possible mechanism of biofilm formation - HPAM degradation - biofilm disappearance and reorganization. Moreover, the degradation rate of strain EPDB-5 on real wastewater containing HPAM was 29.97% in only three days. This work expands our knowledge boundary about the HPAM degradation mechanism at the functional gene level, and supports the potential of strain EPDB-5 as a novel auxiliary microbial resource for the practical application of HPAM.},
}
@article {pmid39413681,
year = {2024},
author = {Wu, X and Qin, L and Song, M and Zhang, C and Guo, J and Yang, Z and Gao, Z and Qiu, M},
title = {Metagenomics combined with untargeted metabolomics to study the mechanism of miRNA-150-5p on SiO2 -induced acute lung injury.},
journal = {Journal of pharmaceutical and biomedical analysis},
volume = {252},
number = {},
pages = {116515},
doi = {10.1016/j.jpba.2024.116515},
pmid = {39413681},
issn = {1873-264X},
abstract = {Acute lung injury is a significant global health issue, and its treatment is becoming a hot topic of the researchers. To investigate the feasibility of miRNA-150-5p tail vein injection in the treatment of SiO2-induced acute lung injury through the regulation of gut microbiota and serum metabolites based on multiomics technology. Twenty-four mice were randomly divided into the control, SiO2 and miRNA-150-5p intervention groups. The SiO2 and miRNA-150-5p intervention groups received a single intranasal dose of 100 µL 4 % SiO2 suspension. Meanwhile, the miRNA-150-5p intervention group was administered with two tail vein injections of miRNA-150-5p (15 nmol each per mouse) on the day of successful modelling and on the third day post modelling. Metagenomics and metabolomics techniques were used to measure gut microbiota and serum metabolites, respectively. Tail vein injection of miRNA-150-5p improved SiO2-induced acute lung injury and reduced the secretion of inflammatory factors interleukin (IL)-6, tumour necrosis factor-α and IL-1β. These conditions altered the structure of gut microbiota, which resulted in the notable modulation of eight species at the species level. In addition, tail vein injection of miRNA-150-5p considerably reduced the levels of substances, such as phosphatidylethanolamine, phosphatidylcholine and phosphatidylinositol, in the glycerophospholipid metabolism and glycosylphosphatidylinositol-anchor biosynthesis pathways. Tail vein injection of miRNA-150-5p can alleviate acute lung injury. Combined metagenomics and untargeted metabolomics revealed the miRNA-150-5p-mitigated SiO2-induced acute lung injury that occurred through the regulation of gut microbiota and serum metabolites.},
}
@article {pmid39413245,
year = {2024},
author = {Wang, L and Yin, Z and Yan, W and Hao, J and Tian, F and Shi, J},
title = {Nitrate-dependent antimony oxidase in an uncultured Symbiobacteriaceae member.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae204},
pmid = {39413245},
issn = {1751-7370},
abstract = {Autotrophic antimony (Sb) oxidation coupled to nitrate reduction plays an important role in the transformation and detoxification of Sb. However, the specific oxidase involved in this process has yet to be identified. Herein, we enriched the microbiota capable of nitrate-dependent Sb(III) oxidation and identified a new Sb(III) oxidase in an uncultured member of Symbiobacteriaceae. Incubation experiments demonstrated that nitrate-dependent Sb(III) oxidation occurred in the microcosm supplemented with Sb(III) and nitrate. Both the 16S rRNA gene and metagenomic analyses indicated that a species within Symbiobacteriaceae played a crucial role in this process. Furthermore, carbon-13 isotope labelling with carbon dioxide-fixing Rhodopseudomonas palustris in combination with nanoscale secondary ion mass spectrometry revealed that a newly characterized oxidase from the dimethylsulfoxide reductase family, designated as NaoABC, was responsible for autotrophic Sb(III) oxidation coupled with nitrate reduction. The NaoABC complex functions in conjunction with the nitrate reductase NarGHI, forming a redox loop that transfers electrons from Sb(III) to nitrate, thereby generating the energy necessary for autotrophic growth. This research offers new insights into the understanding of how microbes link Sb and nitrogen biogeochemical cycles in the environment.},
}
@article {pmid39413127,
year = {2024},
author = {Balinandi, S and Mulei, S and Whitmer, S and Nyakarahuka, L and Cossaboom, CM and Shedroff, E and Morales-Betoulle, M and Krapiunaya, I and Tumusiime, A and Kyondo, J and Baluku, J and Namanya, D and Torach, CR and Mutesi, J and Kiconco, J and Pimundu, G and Muyigi, T and Rowland, J and Nsawotebba, A and Ssewanyana, I and Muwanguzi, D and Kadobera, D and Harris, JR and Ario, AR and Atek, K and Kyobe, HB and Nabadda, S and Kaleebu, P and Mwebesa, HG and Montgomery, JM and Shoemaker, TR and Lutwama, JJ and Klena, JD},
title = {Crimean-Congo hemorrhagic fever cases diagnosed during an outbreak of Sudan virus disease in Uganda, 2022-23.},
journal = {PLoS neglected tropical diseases},
volume = {18},
number = {10},
pages = {e0012595},
doi = {10.1371/journal.pntd.0012595},
pmid = {39413127},
issn = {1935-2735},
abstract = {BACKGROUND: In September 2022, Uganda experienced an outbreak of Sudan virus disease (SVD), mainly in central Uganda. As a result of enhanced surveillance activities for Ebola disease, samples from several patients with suspected viral hemorrhagic fever (VHF) were sent to the VHF Program at Uganda Virus Research Institute (UVRI), Entebbe, Uganda, and identified with infections caused by other viral etiologies. Herein, we report the epidemiologic and laboratory findings of Crimean-Congo hemorrhagic fever (CCHF) cases that were detected during the SVD outbreak response.<br><br>METHODOLOGY: Whole blood samples from VHF suspected cases were tested for Sudan virus (SUDV) by real-time reverse transcription-polymerase chain reaction (RT-PCR); and if negative, were tested for CCHF virus (CCHFV) by RT-PCR. CCHFV genomic sequences generated by metagenomic next generation sequencing were analyzed to ascertain strain relationships.<br><br>PRINCIPAL FINDINGS: Between September 2022 and January 2023, a total of 2,626 samples were submitted for VHF testing at UVRI. Overall, 13 CCHF cases (including 7 deaths; case fatality rate of 53.8%), aged 4 to 60 years, were identified from 10 districts, including several districts affected by the SVD outbreak. Four cases were identified within the Ebola Treatment Unit (ETU) at Mubende Hospital. Most CCHF cases were males engaged in livestock farming or had exposure to wildlife (n = 8; 61.5%). Among confirmed cases, the most common clinical symptoms were hemorrhage (n = 12; 92.3%), fever (n = 11; 84.6%), anorexia (n = 10; 76.9%), fatigue (n = 9; 69.2%), abdominal pain (n = 9; 69.2%) and vomiting (n = 9; 69.2%). Sequencing analysis showed that the majority of identified CCHFV strains belonged to the Africa II clade previously identified in Uganda. Two samples, however, were identified with greater similarity to a CCHFV strain that was last reported in Uganda in 1958, suggesting possible reemergence.<br><br>CONCLUSIONS/SIGNIFICANCE: Identifying CCHFV from individuals initially suspected to be infected with SUDV emphasizes the need for comprehensive VHF testing during filovirus outbreak responses in VHF endemic countries. Without expanded testing, CCHFV-infected patients would have posed a risk to health care workers and others while receiving treatment after a negative filovirus diagnosis, thereby complicating response dynamics. Additionally, CCHFV-infected cases could acquire an Ebola infection while in the ETU, and upon release because of a negative Ebola virus result, have the potential to spread these infections in the community.},
}
@article {pmid39411387,
year = {2024},
author = {Zhao, J and Wang, C and Hu, J and Ma, R and Yu, B and Zhao, W and Wang, H and Gu, Y and Zhang, J},
title = {Integrated metagenomics and metabolomics analyses revealed biomarkers in β-casein A2A2-type cows.},
journal = {Frontiers in veterinary science},
volume = {11},
number = {},
pages = {1438717},
pmid = {39411387},
issn = {2297-1769},
abstract = {In Holstein cows, β-casein, one of the most critical proteins in milk, exists in two main genotypes, A1 and A2. Herein, 45 Holstein cows [categorized into three groups based on β-casein A1A1, A1A2, and A2A2 genotypes (N = 15)] with the same feeding management and litter size were enrolled to explore differences in rumen microflora and metabolites across various β-casein genotypes. Rumen fluids were collected for metagenomics and metabolomics analyses. Metabolomics and weighted gene co-expression network analysis (WGCNA) revealed that arachidonic acid (AA), adrenic acid (AdA), glycocholic acid (GCA), and taurocholic acid (TCA) were significantly and positively correlated with milk fat % in dairy cows (p < 0.05). Furthermore, macro-genomics and Spearman's correlation analysis revealed significant positive correlations (p < 0.05) between the characteristic flora (g_Acetobacter, g_Pseudoxanthomonas, g_Streptococcus, and g_Pediococcus) and the five characteristic metabolites in the rumen of A2A2 dairy cows. Moreover, functional enrichment analysis revealed more genes enriched to the TRP channel's inflammatory mediator-regulated pathway and the mTOR signaling pathway in A2A2 genotyped cows. Additionally, the regulatory effects of AA on bovine mammary epithelial cells (BMECs) were examined using CCK-8, EdU, and qRT-PCR assays, revealing that AA promoted triglyceride (TG) synthesis and upregulated the milk fat marker genes including SREBF1, ACSS2, AGPAT6, and FASN. Overall, we identified characteristic microorganisms and metabolites in A2A2 Holstein cows and established that AA could be a biomarker for higher milk fat %.},
}
@article {pmid39411197,
year = {2024},
author = {Baumann, KBL and Mazzoli, A and Salazar, G and Ruscheweyh, HJ and Müller, B and Niederdorfer, R and Sunagawa, S and Lever, MA and Lehmann, MF and Bürgmann, H},
title = {Metagenomic and -transcriptomic analyses of microbial nitrogen transformation potential, and gene expression in Swiss lake sediments.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae110},
pmid = {39411197},
issn = {2730-6151},
abstract = {The global nitrogen (N) cycle has been strongly altered by anthropogenic activities, including increased input of bioavailable N into aquatic ecosystems. Freshwater sediments are hotspots with regards to the turnover and elimination of fixed N, yet the environmental controls on the microbial pathways involved in benthic N removal are not fully understood. Here, we analyze the abundance and expression of microbial genes involved in N transformations using metagenomics and -transcriptomics across sediments of 12 Swiss lakes that differ in sedimentation rates and trophic regimes. Our results indicate that microbial N loss in these sediments is primarily driven by nitrification coupled to denitrification. N-transformation gene compositions indicated three groups of lakes: agriculture-influenced lakes characterized by rapid depletion of oxidants in the sediment porewater, pristine-alpine lakes with relatively deep sedimentary penetration of oxygen and nitrate, and large, deep lakes with intermediate porewater hydrochemical properties. Sedimentary organic matter (OM) characteristics showed the strongest correlations with the community structure of microbial N-cycling communities. Most transformation pathways were expressed, but expression deviated from gene abundance and did not correlate with benthic geochemistry. Cryptic N-cycling may maintain transcriptional activity even when substrate levels are below detection. Sediments of large, deep lakes generally showed lower in-situ N gene expression than agriculture-influenced lakes, and half of the pristine-alpine lakes. This implies that prolonged OM mineralization in the water column can lead to the suppression of benthic N gene expression.},
}
@article {pmid39410870,
year = {2024},
author = {Matsubara, K and Li, J and Enomoto, Y and Takahashi, T and Ma, M and Ninomiya, R and Kazami, D and Miura, K and Hirayama, K},
title = {Beneficial Role of Heat-Treated Lactobacillus sakei HS-1 on Growth Performance, Nutritional Status and Gut Microbiota in Weaned Piglets.},
journal = {Journal of animal physiology and animal nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpn.14056},
pmid = {39410870},
issn = {1439-0396},
support = {//The authors received no specific funding for this work./ ; },
abstract = {In the swine industry, there is a strong need to replace an antibiotic growth promoter (AGP) used as feed additives in weaned piglets to enhance nutrient utilization in their diets and improve growth performance. Lactobacillus sakei HS-1 strain is a microbial preparation isolated from pickles. The study aim is to investigate the effectiveness of heat-treated L. sakei HS-1 strain (HT-LS) as a growth promoter in weaned piglets compared to colistin (CS), a widely used AGP. Eighteen crossbred weaned piglets (Landrace × Yorkshire × Duroc) of 21 days (average body weight [BW]: 7.06 ± 0.59 kg) were divided into three groups: fed the control diet (CT group), fed a diet supplemented with 30 ppm colistin sulphate (CS group), fed a diet supplemented with HT-LS at a concentration of 2.0 × 10[5] cells/g (LS group) until 49 days. The results indicated that LS group exhibited significantly higher average daily gain (p < 0.05) and higher BW (p < 0.1) compared with CT group, even higher than CS group. CS group showed higher growth performance compared to CT group but the differences were not statistically significant. In addition, LS group had higher (p < 0.05) or tended to higher (p < 0.1) concentrations of several plasma amino acids than the other two groups at 35 and 49 days. Faecal acetate concentration was higher (p < 0.1) in LS group than in CT group at 35 days. Blood immunoglobulin G concentration in LS group was significantly lower (p < 0.05) than in CT group at 35 and 49 days, and blood immunoglobulin A tended to be lower (p < 0.1) at 35 days than in CT group. LS group showed an increased abundance of g_Prevotella 7, g_Streptococcus and g_Lactobacillus (linear discriminant analysis [LDA] score ≥ 2.0). Predictive metagenomic analysis revealed an enrichment of the mixed acid fermentation pathway (LDA score ≥ 2.0). Furthermore, several gut microbes exhibited correlations with plasma amino acids (p < 0.01) and short-chain fatty acids in faeces (p < 0.01). These findings demonstrate that HT-LS improves the growth performance of weaned piglets by enhancing the efficient utilization of nutrients through gut microbiota modification.},
}
@article {pmid39410242,
year = {2024},
author = {Wang, B and Wu, W and Wang, Z and Chen, Z and Wang, X},
title = {Soil-Mulching Treatment Enhances the Content of Stilbene in Grape Berries: A Transcriptomic and Metabolomic Analysis.},
journal = {Foods (Basel, Switzerland)},
volume = {13},
number = {19},
pages = {},
doi = {10.3390/foods13193208},
pmid = {39410242},
issn = {2304-8158},
support = {[CX(21)2027]//Jiangsu Agricultural Science and Technology Innovation Fund/ ; },
abstract = {Soil mulching is a useful agronomic practice that promotes early fruit maturation and affects fruit quality. However, the regulatory mechanism of fruit metabolites under soil-mulching treatments remains unknown. In this study, variations in the gene sets and metabolites of grape berries after mulching (rice straw + felt + plastic film) using transcriptome and metagenomic sequencing were investigated. The results of the cluster analysis and orthogonal projection to latent structures discriminant analysis of the metabolites showed a difference between the mulching and control groups, as did the principal component analysis results for the transcriptome. In total, 36 differentially expressed metabolites were identified, of which 10 (resveratrol, ampelopsin F, piceid, 3,4'-dihydroxy-5-methoxystilbene, ε-viniferin, trans resveratrol, epsilon-viniferin, 3'-hydroxypterostilbene, 1-methyl-resveratrol, and pterostil-bene) were stilbenes. Their content increased after mulching, indicating that stilbene synthase activity increased after mulching. The weighted gene co-expression network analysis revealed that the turquoise and blue modules were positively and negatively related to stilbene compounds. The network analysis identified two seed genes (VIT_09s0054g00610, VIT_13s0156g00260) and two transcription factors (VIT_13s0156g00260, VIT_02s0025g04590). Overall, soil mulching promoted the accumulation of stilbene compounds in grapes, and the results provided key genetic information for further studies.},
}
@article {pmid39410228,
year = {2024},
author = {Kim, S and Kang, JY and Nguyen, QA and Lee, JS},
title = {Effects of Prebiotic Dietary Fibers on the Stimulation of the Mucin Secretion in Host Cells by In Vitro Gut Microbiome Consortia.},
journal = {Foods (Basel, Switzerland)},
volume = {13},
number = {19},
pages = {},
doi = {10.3390/foods13193194},
pmid = {39410228},
issn = {2304-8158},
support = {NRF-2021R1A2C1005811//National Research Foundation of Korea/ ; NRF-2023K2A9A1A01098813, FY2023//National Research Foundation of Korea/ ; KRIBB Research Initiative Program grant (KGM5482423)//Korea Research Institute of Bioscience and Biotechnology/ ; },
abstract = {The gastrointestinal microbiota are important for human health. Dietary intake may modulate the composition and metabolic function of the gut microbiome. We examined how the breakdown of prebiotic dietary fibers by the gut microbiome affects mucin secretion by intestinal epithelial cells. Metagenomic analyses of in vitro gut microbiome consortia revealed taxonomic profiles and genetic diversity of carbohydrate-active enzymes that digest polysaccharides. Two independent consortia exhibited different abilities to produce acetic acid, propionic acid, and butyric acid via the fermentation of polysaccharides derived from dietary fibers of grains and mushrooms. Although acetic acid generally had the highest concentration, the ratios of butyric acid and propionic acid to acetic acid varied depending on the polysaccharide source. These short-chain fatty acids affected morphological differentiation and mucin secretion in HT-29 human intestinal epithelial cells. These results suggest that prebiotic dietary fibers can be digested and metabolized by the gut microbiome to short-chain fatty acids, which can affect gut epithelial cells both directly and indirectly via the modulation of the gut microbiota and their enzymes.},
}
@article {pmid39410210,
year = {2024},
author = {Liang, J and Yuan, H and Fei, Y and Wang, H and Qu, C and Bai, W and Liu, G},
title = {Effects of Saccharomyces cerevisiae and Cyberlindnera fabianii Inoculation on Rice-Flavor Baijiu Fermentation.},
journal = {Foods (Basel, Switzerland)},
volume = {13},
number = {19},
pages = {},
doi = {10.3390/foods13193175},
pmid = {39410210},
issn = {2304-8158},
support = {2021ZDJS005//the Research Capacity Enhancement Project of Key Disciplines in Guangdong Province/ ; 2023KJ101//Guangdong Provincial Agricultural Science and Technology Innovation and Extension Project in 2023/ ; 2021B1212040013//Guangdong Provincial Key Laboratory of Lingnan Specialty Food Science and Technology/ ; },
abstract = {Rice-flavor baijiu is a distilled Chinese spirit prepared from Xiaoqu culture. However, its dull taste may be a market limitation. In order to enhance the flavor profile of rice-flavor baijiu, two ester-producing yeast strains (Saccharomyces cerevisiae and Cyberlindnera fabianii) were inoculated for fermentation. At the end of the fermentation, the total alcohol and ester contents had also increased by 43.3% and 29.8%, respectively, and the number of ester species had increased by eight. Additionally, eleven flavor substances had significant contributions in the inoculated fermentation process, including several different esters and alcohols. A macrogenomic analysis revealed that the majority of the gene abundances associated with the alcohol, acid, and ester pathways were elevated by the third day of inoculated fermentation, and greater abundances of Saccharomyces cerevisiae, Cyberlindnera fabianii, Lichtheimia ramosa, Rhizopus delemar, and Rhizopus oryzaefive, annotated with these genes, were observed from either the pre-fermentation stage or post-fermentation stage. The results demonstrate that two added strains are associated with an increase in the content of the flavor substances. These findings may prove beneficial in enhancing the quality of rice-flavor baijiu through using inoculated fermentation with ester-producing yeast.},
}
@article {pmid39410149,
year = {2024},
author = {Liang, Z and Chen, S and Wang, H and Wu, Q and Guo, W and Ni, L and Lv, X},
title = {Metagenomic and Metabolomic Profiling Reveals the Differences of Flavor Quality between Hongqu Rice Wines Fermented with Gutian Qu and Wuyi Qu.},
journal = {Foods (Basel, Switzerland)},
volume = {13},
number = {19},
pages = {},
doi = {10.3390/foods13193114},
pmid = {39410149},
issn = {2304-8158},
support = {No. 32472296; No. 32472295; No. 32072204//National Natural Science Foundation of China/ ; },
abstract = {Jiuqu (starter) makes an important contribution to the formation of the flavor characteristics of Hongqu rice wine (HQW). Gutian Qu (GTQ) and Wuyi Qu (WYQ) are two kinds of Jiuqu commonly used in HQW brewing, but the comparison of the two kinds of HQW is still insufficient at present. The objective of this study was to compare the dynamic changes of amino acids (AAs), higher alcohols (HAs), bioamines (BAs), volatile flavor compounds (VFCs), and microbial communities in HQW fermentation, with GTQ and WYQ as starter. This study used an automatic amino acid analyzer, GC, HPLC, and GC-MS to detect AAs, HAs, Bas, and VFCs during fermentation; metagenomic sequencing technology was used to elucidate the microbial community and its functional characteristics. The results showed that the contents of AAs and HAs in HQW brewed with WYQ (WYW) were significantly higher than those in HQW brewed with GTQ (GTW). On the contrary, the majority of BAs in GTW were significantly higher than those in WYW. The composition of VFCs in WYW and GTW were obviously different, as most of the VFCs were notably enriched in WYW, while ethyl caproate, isoamyl acetate, ethyl heptanoate, ethyl nonanoate, 1-decanol, citronellol, phenethyl acetate, and hexanoic acid were more abundant in GTW. Burkholderia gladioli, Pantoea dispersa, Weissella cibaria, Monascus purpureus, and Saccharomyces cerevisiae were the predominant microbial populations in GTW brewing at the species level, while Sphingomonas sp., Kosakonia cowanii, Enterobacter asburiae, Leuconostoc lactis, Aspergillus niger, and Saccharomyces cerevisiae were the dominant microbial species in WYW brewing. The abundance of functional genes involved in BAs biosynthesis were much higher in GTW brewing, while the abundance of functional genes related to the metabolism of characteristic VFCs were much higher in WYW brewing. Collectively, these findings provided evidence for elucidating the effects of Jiuqu and microbial communities on HQW flavor quality, and laid a solid foundation for the improvement of HQW flavor quality.},
}
@article {pmid39409842,
year = {2024},
author = {Xie, M and Fei, D and Guang, Y and Xue, F and Xu, J and Zhou, Y},
title = {Role of Metabolomics and Metagenomics in the Replacement of the High-Concentrate Diet with a High-Fiber Diet for Growing Yushan Pigs.},
journal = {Animals : an open access journal from MDPI},
volume = {14},
number = {19},
pages = {},
doi = {10.3390/ani14192893},
pmid = {39409842},
issn = {2076-2615},
support = {2021BDH80013//the Science and Technology Cooperation Program of Jiangxi/ ; 20192ACB60004//the Jiangxi Key Research and Development Program/ ; 2024SSY04211//the safe quality of agricultural products key laboratory of Jiangxi Province/ ; },
abstract = {The objective of this study was to investigate the regulatory effects of a high-fiber content feed on the productive performance, meat quality, and fat acid composition. A total of 18 120-day-old Yushan pigs with similar initial body weight were randomly allotted into high-concentrate diet (high energy, HE) and high-fiber diet (low energy, LE) treatments for the determination of regulatory effects on productive performance, meat quality, and fatty acid content. Further, blood metabolomic, gut microbiota, and liver energy-related gene expression measurements were used to investigate the underlying mechanisms. Results showed that the LE treatment significantly increased ADFI while decreasing carcass weight, fat percentage, and IMF. Metabolomic results showed that the high-fiber treatment significantly down-regulated metabolites that participated in lipid metabolism such as cyclic ADP-ribose and hippuric acid, while up-regulated metabolites were mainly enriched in nitrogen metabolism such as DL-arginine and propionylcarnitine (p < 0.05). Microbial results showed relative abundances of Lactobacillus and Bifidobacterium are significantly proliferated in the high-fiber feeding treatments (p < 0.05). Transcriptomic results showed that genes mainly enriched into the lipid metabolism are significantly up-regulated under the high-fiber dietary treatment (p < 0.05). Conclusion: higher dietary fiber significantly reduced dietary energy provision, effectively decreased the backfat and abdominal fat content of Yushan pigs through proliferating intestinal fiber-degradable bacteria, and up-regulating the hepatic lipolysis-related gene expression.},
}
@article {pmid39409167,
year = {2024},
author = {Evseev, P and Gutnik, D and Evpak, A and Kasimova, A and Miroshnikov, K},
title = {Origin, Evolution and Diversity of φ29-like Phages-Review and Bioinformatic Analysis.},
journal = {International journal of molecular sciences},
volume = {25},
number = {19},
pages = {},
doi = {10.3390/ijms251910838},
pmid = {39409167},
issn = {1422-0067},
mesh = {*Bacteriophages/genetics/classification ; *Computational Biology/methods ; *Genome, Viral ; Evolution, Molecular ; Phylogeny ; Archaea/virology/genetics ; Capsid Proteins/genetics ; },
abstract = {Phage φ29 and related bacteriophages are currently the smallest known tailed viruses infecting various representatives of both Gram-positive and Gram-negative bacteria. They are characterised by genomic content features and distinctive properties that are unique among known tailed phages; their characteristics include protein primer-driven replication and a packaging process characteristic of this group. Searches conducted using public genomic databases revealed in excess of 2000 entries, including bacteriophages, phage plasmids and sequences identified as being archaeal that share the characteristic features of phage φ29. An analysis of predicted proteins, however, indicated that the metagenomic sequences attributed as archaeal appear to be misclassified and belong to bacteriophages. An analysis of the translated polypeptides of major capsid proteins (MCPs) of φ29-related phages indicated the dissimilarity of MCP sequences to those of almost all other known Caudoviricetes groups and a possible distant relationship to MCPs of T7-like (Autographiviridae) phages. Sequence searches conducted using HMM revealed the relatedness between the main structural proteins of φ29-like phages and an unusual lactococcal phage, KSY1 (Chopinvirus KSY1), whose genome contains two genes of RNA polymerase that are similar to the RNA polymerases of phages of the Autographiviridae and Schitoviridae (N4-like) families. An analysis of the tail tube proteins of φ29-like phages indicated their dissimilarity of the lower collar protein to tail proteins of all other viral groups, but revealed its possible distant relatedness with proteins of toxin translocation complexes. The combination of the unique features and distinctive origin of φ29-related phages suggests the categorisation of this vast group in a new order or as a new taxon of a higher rank.},
}
@article {pmid39409144,
year = {2024},
author = {Donchev, D and Stoikov, I and Diukendjieva, A and Ivanov, IN},
title = {Assessment of Skimmed Milk Flocculation for Bacterial Enrichment from Water Samples, and Benchmarking of DNA Extraction and 16S rRNA Databases for Metagenomics.},
journal = {International journal of molecular sciences},
volume = {25},
number = {19},
pages = {},
doi = {10.3390/ijms251910817},
pmid = {39409144},
issn = {1422-0067},
support = {BG05M2OP001-1.002-0001-C04//European Regional Development Fund through the Operational Program Science and Education for Smart Growth 2014-2020/ ; not applicable//Biocampus Sofia Association/ ; },
mesh = {*RNA, Ribosomal, 16S/genetics ; *Milk/microbiology ; *Metagenomics/methods ; Animals ; *DNA, Bacterial/genetics/isolation &amp; purification ; *Bacteria/genetics/classification/isolation &amp; purification ; Flocculation ; Benchmarking ; Microbiota/genetics ; Water Microbiology ; },
abstract = {Water samples for bacterial microbiome studies undergo biomass concentration, DNA extraction, and taxonomic identification steps. Through benchmarking, we studied the applicability of skimmed milk flocculation (SMF) for bacterial enrichment, an adapted in-house DNA extraction protocol, and six 16S rRNA databases (16S-DBs). Surface water samples from two rivers were treated with SMF and vacuum filtration (VF) and subjected to amplicon or shotgun metagenomics. A microbial community standard underwent five DNA extraction protocols, taxonomical identification with six different 16S-DBs, and evaluation by the Measurement Integrity Quotient (MIQ) score. In SMF samples, the skimmed milk was metabolized by members of lactic acid bacteria or genera such as Polaromonas, Macrococcus, and Agitococcus, resulting in increased relative abundance (p < 0.5) up to 5.0 log fold change compared to VF, rendering SMF inapplicable for bacterial microbiome studies. The best-performing DNA extraction protocols were FastSpin Soil, the in-house method, and EurX. All 16S-DBs yielded comparable MIQ scores within each DNA extraction kit, ranging from 61-66 (ZymoBIOMICs) up to 80-82 (FastSpin). DNA extraction kits exert more bias toward the composition than 16S-DBs. This benchmarking study provided valuable information to inform future water metagenomic study designs.},
}
@article {pmid39409119,
year = {2024},
author = {Xiang, J and Zhang, N and Li, J and Zhu, Y and Cao, T and Wang, Y},
title = {Unveiling the Hidden Responses: Metagenomic Insights into Dwarf Bamboo (Fargesia denudata) Rhizosphere under Drought and Nitrogen Challenges.},
journal = {International journal of molecular sciences},
volume = {25},
number = {19},
pages = {},
doi = {10.3390/ijms251910790},
pmid = {39409119},
issn = {1422-0067},
support = {2019QZKK0303//the Second Tibetan Plateau Scientific Expedition and Research Program (STEP)/ ; 31470621//National Natural Science Foundation of China/ ; },
mesh = {*Rhizosphere ; *Nitrogen/metabolism ; *Droughts ; *Metagenomics/methods ; Soil Microbiology ; Metagenome ; Stress, Physiological/genetics ; Poaceae/genetics/microbiology ; Plant Roots/microbiology/genetics ; Soil/chemistry ; },
abstract = {Dwarf bamboo (Fargesia denudata) is a crucial food source for the giant pandas. With its shallow root system and rapid growth, dwarf bamboo is highly sensitive to drought stress and nitrogen deposition, both major concerns of global climate change affecting plant growth and rhizosphere environments. However, few reports address the response mechanisms of the dwarf bamboo rhizosphere environment to these two factors. Therefore, this study investigated the effects of drought stress and nitrogen deposition on the physicochemical properties and microbial community composition of the arrow bamboo rhizosphere soil, using metagenomic sequencing to analyze functional genes involved in carbon and nitrogen cycles. Both drought stress and nitrogen deposition significantly altered the soil nutrient content, but their combination had no significant impact on these indicators. Nitrogen deposition increased the relative abundance of the microbial functional gene nrfA, while decreasing the abundances of nirK, nosZ, norB, and nifH. Drought stress inhibited the functional genes of key microbial enzymes involved in starch and sucrose metabolism, but promoted those involved in galactose metabolism, inositol phosphate metabolism, and hemicellulose degradation. NO3[-]-N showed the highest correlation with N-cycling functional genes (p < 0.01). Total C and total N had the greatest impact on the relative abundance of key enzyme functional genes involved in carbon degradation. This research provides theoretical and technical references for the sustainable management and conservation of dwarf bamboo forests in giant panda habitats under global climate change.},
}
@article {pmid39408280,
year = {2024},
author = {Nguyen, SM and Tran, TDC and Tran, TM and Wang, C and Wu, J and Cai, Q and Ye, F and Shu, XO},
title = {Influence of Peanut Consumption on the Gut Microbiome: A Randomized Clinical Trial.},
journal = {Nutrients},
volume = {16},
number = {19},
pages = {},
doi = {10.3390/nu16193313},
pmid = {39408280},
issn = {2072-6643},
support = {N/A//The Peanut Institute/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Arachis ; Male ; Female ; *Feces/microbiology ; Adult ; Bacteria/classification/genetics ; Vietnam ; Diet ; Middle Aged ; },
abstract = {Background: Peanut consumption could impact cardiometabolic health through gut microbiota, a hypothesis that remains to be investigated. A randomized clinical trial in Vietnam evaluated whether peanut consumption alters gut microbiome communities. Methods: One hundred individuals were included and randomly assigned to the peanut intervention and control groups. A total of 51 participants were provided with and asked to consume 50 g of peanuts daily, while 49 controls maintained their usual dietary intake for 16 weeks. Stool samples were collected before and on the last day of the trial. After excluding 22 non-compliant participants and those who received antibiotic treatment, 35 participants from the intervention and 43 from the control were included in the analysis. Gut microbiota composition was measured by shotgun metagenomic sequencing. Associations of changes in gut microbial diversity with peanut intervention were evaluated via linear regression analysis. Linear mixed-effects models were used to analyze associations of composition, sub-community structure, and microbial metabolic pathways with peanut intervention. We also performed beta regression analysis to examine the impact of peanut intervention on the overall and individual stability of microbial taxa and metabolic pathways. All associations with false discovery rate (FDR)-corrected p-values of <0.1 were considered statistically significant. Results: No significant changes were found in α- and β-diversities and overall gut microbial stability after peanut intervention. However, the peanut intervention led to lower enrichment of five phyla, five classes, two orders, twenty-four metabolic pathways, and six species-level sub-communities, with a dominant representation of Bifidobacterium pseudocatenulatum, Escherichia coli D, Holdemanella biformis, Ruminococcus D bicirculans, Roseburia inulinivorans, and MGYG-HGUT-00200 (p < 0.05 and FDR < 0.1). The peanut intervention led to the short-term stability of several species, such as Faecalibacterium prausnitzii F and H, and a metabolic pathway involved in nitrate reduction V (p < 0.05; FDR < 0.1), known for their potential roles in human health, especially cardiovascular health. Conclusions: In summary, a 16-week peanut intervention led to significant changes in gut microbial composition, species-level sub-communities, and the short-term stability of several bacteria, but not overall gut microbial diversity and stability. Further research with a larger sample size and a longer intervention period is needed to confirm these findings and investigate the direct impact of gut-microbiome-mediated health effects of peanut consumption. Trial registration: The International Traditional Medicine Clinical Trial Registry (ITMCTR). Registration number: ITMCTR2024000050. Retrospectively Registered 24 April 2024.},
}
@article {pmid39407862,
year = {2024},
author = {Alavi, SMA and Petri, F and Mahmoud, OK and Igwilo-Alaneme, R and El Zein, S and Nassr, AN and Gori, A and Berbari, EF},
title = {Culture-Negative Native Vertebral Osteomyelitis: A Narrative Review of an Underdescribed Condition.},
journal = {Journal of clinical medicine},
volume = {13},
number = {19},
pages = {},
doi = {10.3390/jcm13195802},
pmid = {39407862},
issn = {2077-0383},
abstract = {The incidence of culture-negative NVO (CN-NVO) cases is increasing, presenting significant diagnostic and therapeutic challenges due to the inability to isolate causative organisms with conventional microbiological methods. Factors influencing the diagnosis of CN-NVO include prior antimicrobial therapy, low pathogen burden, fastidious or intracellular organisms, technical issues, and non-infectious mimickers. Diagnosis often relies on imaging modalities like magnetic resonance imaging (MRI) and computed tomography (CT)-guided biopsy, though these methods can sometimes fail to yield positive microbiological results. Advanced diagnostic tools, such as polymerase chain reaction (PCR), metagenomic next-generation sequencing (mNGS), and cell-free DNA analysis, may be necessary to identify the pathogen. The causative pathogen cannot be isolated in some patients, among which an empirical antimicrobial therapy should be initiated. This narrative review discusses the management, monitoring, surgical indications, and outcomes for patients with CN-NVO.},
}
@article {pmid39407853,
year = {2024},
author = {Laryushina, Y and Samoilova-Bedych, N and Turgunova, L and Kozhakhmetov, S and Alina, A and Suieubayev, M and Mukhanbetzhanov, N},
title = {Alterations of the Gut Microbiome and TMAO Levels in Patients with Ulcerative Colitis.},
journal = {Journal of clinical medicine},
volume = {13},
number = {19},
pages = {},
doi = {10.3390/jcm13195794},
pmid = {39407853},
issn = {2077-0383},
support = {AP14871959//Science Committee of the Ministry of Education and Science of the Republic of Kazakhstan/ ; },
abstract = {Background: Ulcerative colitis (UC) is an idiopathic and heterogeneous large intestine disease, characterized by chronic mucosa and submucosa inflammation. Alteration of the intestinal microbiome in UC may be responsible for modifications in metabolite production. Aim: To investigate the microbiota status and trimethylamine-N-oxide (TMAO) metabolite levels in patients with UC according to clinical and endoscopic activity. Methods: As part of a grant project AP14871959 from September 2022 to October 2023, 31 patients with UC and 15 healthy volunteers over 18 years at the Clinic of NCJSC "KMU" were assessed for blood TMAO level and metagenomic sequencing of fecal microbiome. Results: A significant depletion of the main representatives of Bacteroides, Parabacteroides, Prevotella; and an increase in the relative abundance of the genera Actinomyces, Klebsiella, Limosilactobacillus, Streptococcus, Escherichia-Shigella were detected in patients with UC. The number of p_Actinobacteria (g_Collinsella) and p_Eubacterium (g_Xylanophilum) representatives with genes encoding TMA-trimethylamine conversion is significantly reduced in UC patients. TMAO levels were significantly lower in UC patients than in healthy individuals (0.233 µmol/L, p = 0.004). TMAO decreased with disease severity and significantly differed between patients with different activities (p = 0.034). Conclusions: The composition of the intestinal microbiome changes and the level of TMAO decreases in patients with UC at different activities.},
}
@article {pmid39407346,
year = {2024},
author = {Barcenilla, C and Cobo-Díaz, JF and Puente, A and Valentino, V and De Filippis, F and Ercolini, D and Carlino, N and Pinto, F and Segata, N and Prieto, M and López, M and Alvarez-Ordóñez, A},
title = {In-depth characterization of food and environmental microbiomes across different meat processing plants.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {199},
pmid = {39407346},
issn = {2049-2618},
support = {BOCYL-D-07072020-6//Junta de Castilla y Le&#xf3;n and the European Social Fund/ ; PRE2021-098910//Ministerio de Ciencia e Innovaci&#xf3;n, Spain/ ; },
mesh = {*Microbiota ; *Food Microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Meat Products/microbiology ; *Food Handling ; Environmental Microbiology ; Meat/microbiology ; RNA, Ribosomal, 16S/genetics ; Animals ; Phylogeny ; },
abstract = {BACKGROUND: Processing environments can be an important source of pathogenic and spoilage microorganisms that cross contaminate meat and meat products. The aim of this study was to characterize the microbiome of raw materials, processing environments and end products from 19 facilities producing different meat products.<br><br>RESULTS: The taxonomic profiles of the microbial communities evolved along processing, from raw materials to end products, suggesting that food contact (FC) surfaces play an important role in modulating the microbiome of final products. Some species persisted with the highest relative abundance in raw materials, food processing environments and/or in the final product, including species from the genera Pseudomonas, Staphylococcus, Brochothrix, Acinetobacter and Psychrobacter. Processing environments showed a very diverse core microbiota, partially shared with the products. Pseudomonas fragi and Pseudomonas sp. Lz4W (in all sample and facility types) and Brochothrix thermosphacta, Psychrobacter sp. and Psychrobacter sp. P11F6 (in raw materials, FC surfaces and end products) were prominent members of the core microbiota for all facilities, while Latilactobacillus sakei was found as a dominant species exclusively in end products from the facilities producing fermented sausages. Processing environments showed a higher amount of antimicrobial resistance genes and virulence factors than raw materials and end products. One thousand four hundred twenty-one medium/high-quality metagenome-assembled genomes (MAGs) were reconstructed. Of these, 274 high-quality MAGs (completeness&#x2009;>&#x2009;90%) corresponded to 210 putative new species, mostly found in processing environments. For two relevant taxa in meat curing and fermentation processes (S. equorum and L. sakei, respectively), phylogenetic variation was observed associated with the specific processing facility under study, which suggests that specific strains of these taxa may be selected in different meat processing plants, likely contributing to the peculiar sensorial traits of the end products produced in them.<br><br>CONCLUSIONS: Overall, our findings provide the most detailed metagenomics-based perspective up to now of the microbes that thrive in meat, meat products and associated environments and open avenues for future research activities to better understand the microbiome functionality and potential contribution to meat quality and safety. Video Abstract.},
}
@article {pmid39407345,
year = {2024},
author = {Salgado, JFM and Hervé, V and Vera, MAG and Tokuda, G and Brune, A},
title = {Unveiling lignocellulolytic potential: a genomic exploration of bacterial lineages within the termite gut.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {201},
pmid = {39407345},
issn = {2049-2618},
abstract = {BACKGROUND: The microbial landscape within termite guts varies across termite families. The gut microbiota of lower termites (LT) is dominated by cellulolytic flagellates that sequester wood particles in their digestive vacuoles, whereas in the flagellate-free higher termites (HT), cellulolytic activity has been attributed to fiber-associated bacteria. However, little is known about the role of individual lineages in fiber digestion, particularly in LT.<br><br>RESULTS: We investigated the lignocellulolytic potential of 2223 metagenome-assembled genomes (MAGs) recovered from the gut metagenomes of 51 termite species. In the flagellate-dependent LT, cellulolytic enzymes are restricted to MAGs of Bacteroidota (Dysgonomonadaceae, Tannerellaceae, Bacteroidaceae, Azobacteroidaceae) and Spirochaetota (Breznakiellaceae) and reflect a specialization on cellodextrins, whereas their hemicellulolytic arsenal features activities on xylans and diverse heteropolymers. By contrast, the MAGs derived from flagellate-free HT possess a comprehensive arsenal of exo- and endoglucanases that resembles that of termite gut flagellates, underlining that Fibrobacterota and Spirochaetota occupy the cellulolytic niche that became vacant after the loss of the flagellates. Furthermore, we detected directly or indirectly oxygen-dependent enzymes that oxidize cellulose or modify lignin in MAGs of Pseudomonadota (Burkholderiales, Pseudomonadales) and Actinomycetota (Actinomycetales, Mycobacteriales), representing lineages located at the hindgut wall.<br><br>CONCLUSIONS: The results of this study refine our concept of symbiotic digestion of lignocellulose in termite guts, emphasizing the differential roles of specific bacterial lineages in both flagellate-dependent and flagellate-independent breakdown of cellulose and hemicelluloses, as well as a so far unappreciated role of oxygen in the depolymerization of plant fiber and lignin in the microoxic periphery during gut passage in HT. Video Abstract.},
}
@article {pmid39407340,
year = {2024},
author = {Chemel, M and Peru, E and Binsarhan, M and Logares, R and Lartaud, F and Galand, PE},
title = {Cold-water coral mortality under ocean warming is associated with pathogenic bacteria.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {76},
pmid = {39407340},
issn = {2524-6372},
support = {ANR-20-CE02-0006//Agence Nationale de la Recherche/ ; ANR-20-CE02-0006//Agence Nationale de la Recherche/ ; },
abstract = {Cold-water corals form vast reefs that are highly valuable habitats for diverse deep-sea communities. However, as the deep ocean is warming, it is essential to assess the resilience of cold-water corals to future conditions. The effects of elevated temperatures on the cold-water coral Lophelia pertusa (now named Desmophyllum pertusum) from the north-east Atlantic Ocean were experimentally investigated at the holobiont level, the coral host, and its microbiome. We show that at temperature increases of + 3 and + 5 °C, L. pertusa exhibits significant mortality concomitant with changes in its microbiome composition. In addition, a metagenomic approach revealed the presence of gene markers for bacterial virulence factors suggesting that coral death was due to infection by pathogenic bacteria. Interestingly, different coral colonies had different survival rates and, colony-specific microbiome signatures, indicating strong colony-specific variability in their response to warming waters. These results suggest that L. pertusa can only survive a long-term temperature increase of < 3 °C. Therefore, regional variations in deep-sea temperature increase should be considered in future estimates of the global distribution of cold-water corals.},
}
@article {pmid39407289,
year = {2024},
author = {Natasha, A and Pye, SE and Cho, SH and Pangestu, HS and Park, J and Park, K and Prayitno, SP and Kim, B and Lee, JS and Kim, J and Budhathoki, S and Oh, Y and Song, JW and López, CB and Suh, JG and Kim, WK},
title = {Molecular detection and genomic characterization of Samak Micromys paramyxovirus-1 and -2 in Micromys minutus, Republic of Korea.},
journal = {Virology journal},
volume = {21},
number = {1},
pages = {255},
pmid = {39407289},
issn = {1743-422X},
support = {20210466//Korea Institute of Marine Science and Technology promotion/ ; 20210466//Korea Institute of Marine Science and Technology promotion/ ; 20210466//Korea Institute of Marine Science and Technology promotion/ ; 20210466//Korea Institute of Marine Science and Technology promotion/ ; 20210466//Korea Institute of Marine Science and Technology promotion/ ; 20210466//Korea Institute of Marine Science and Technology promotion/ ; 20210466//Korea Institute of Marine Science and Technology promotion/ ; 20210466//Korea Institute of Marine Science and Technology promotion/ ; NF22SA0082041//Novo Nordisk Fonden/ ; NF22SA0082041//Novo Nordisk Fonden/ ; 2023R1A2C2006105//National Research Foundation of Korea/ ; 202300249142//National Research Foundation of Korea/ ; 2023R1A2C2006105//National Research Foundation of Korea/ ; 2023R1A2C2006105//National Research Foundation of Korea/ ; 202300249142//National Research Foundation of Korea/ ; IBS-R801-D9-A03//Institute for Basic Science/ ; IBS-R801-D9-A03//Institute for Basic Science/ ; IBS-R801-D9-A03//Institute for Basic Science/ ; HG23C1623//the Government-wide R&amp;D to Advance Infectious Disease Prevention and Control, Republic of Korea/ ; },
abstract = {BACKGROUND: The discovery of viruses in small mammalian populations, particularly rodents, has expanded the family Paramyxoviridae. The overlap in habitats between rodents and humans increases the risk of zoonotic events, underscoring the importance of active surveillance. Rodent species, such as Apodemus agrarius, are natural hosts for Paramyxoviridae in the Republic of Korea (ROK). However, it is unknown whether Paramyxoviridae is present in Micromys minutus, another common rodent.<br><br>METHOD: Here, we screened M. minutus collected from the Gangwon Province in the ROK for paramyxoviruses using nested polymerase chain reaction and confirm positive samples by next-generation metagenomic sequencing. Complete paramyxovirus genomes were further characterized by phylogenetic analysis, amino acid similarity, secondary structure, and cophylogeny.<br><br>RESULT: Overall, 57 of 145 (39.3%) M. minutus kidney samples tested positive for paramyxoviruses. Among them, four whole genome sequences were identified and clustered within the genus Jeilongvirus. One sequence was determined as Samak Micromys paramyxovirus 1 (SMPV-1; 19,911 nucleotides long) and three sequences as Samak Micromys paramyxovirus 2 (SMPV-2; 18,199 nucleotides long). SMPV-1 has a smaller hydrophobic gene and a longer glycoprotein gene than SMPV-2. Cophylogenetic analysis suggests that SMPV-1 evolved through co-divergence, whereas SMPV-2 was inferred to have undergone transfer events.<br><br>CONCLUSION: These findings highlight the prevalence of paramyxoviruses in the wild and the potential of M. minutus as a natural viral reservoir. The discovery of SMPV-1 and SMPV -&#x2009;2 also reveals the genetic diversity and evolutionary history of the genus Jeilongvirus in the Paramyxoviridae.},
}
@article {pmid39406897,
year = {2024},
author = {Westmeijer, G and van Dam, F and Kietäväinen, R and González-Rosales, C and Bertilsson, S and Drake, H and Dopson, M},
title = {Candidatus Desulforudis audaxviator dominates a 975 m deep groundwater community in central Sweden.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {1332},
pmid = {39406897},
issn = {2399-3642},
support = {2018-04311//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; },
mesh = {*Groundwater/microbiology ; Sweden ; Microbiota/genetics ; Metagenome ; Phylogeny ; Deltaproteobacteria/genetics/classification/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The continental bedrock contains groundwater-bearing fractures that are home to microbial populations that are vital in mediating the Earth's biogeochemical cycles. However, their diversity is poorly understood due to the difficulty of obtaining samples from this environment. Here, a groundwater-bearing fracture at 975 m depth was isolated by employing packers in order to characterize the microbial community via metagenomes combined with prokaryotic and eukaryotic marker genes (16S and 18S ribosomal RNA gene). Genome-resolved analyses revealed a community dominated by sulfate-reducing Bacillota, predominantly represented by Candidatus Desulforudis audaxviator and with Wood-Ljungdahl as the most prevalent pathway for inorganic carbon fixation. Moreover, the eukaryotic community had a considerable diversity and was comprised of mainly flatworms, chlorophytes, crustaceans, ochrophytes, and fungi. These findings support the important role of the Bacillota, with the sulfate reducer Candidatus Desulforudis audaxviator as its main representative, as primary producers in the often energy-limited groundwaters of the continental subsurface.},
}
@article {pmid39406702,
year = {2024},
author = {Wegner, H and Roitman, S and Kupczok, A and Braun, V and Woodhouse, JN and Grossart, HP and Zehner, S and Béjà, O and Frankenberg-Dinkel, N},
title = {Identification of Shemin pathway genes for tetrapyrrole biosynthesis in bacteriophage sequences from aquatic environments.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {8783},
pmid = {39406702},
issn = {2041-1723},
support = {FR1487/16-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 143/18//Israel Science Foundation (ISF)/ ; },
mesh = {*Tetrapyrroles/biosynthesis/metabolism ; *Bacteriophages/genetics/metabolism ; Escherichia coli/genetics/virology/metabolism ; 5-Aminolevulinate Synthetase/genetics/metabolism ; Amino Acid Sequence ; Heme/metabolism/biosynthesis ; Aminolevulinic Acid/metabolism ; Phylogeny ; Fresh Water/virology ; Biosynthetic Pathways/genetics ; },
abstract = {Tetrapyrroles such as heme, chlorophyll, and vitamin B12 are essential for various metabolic pathways. They derive from 5-aminolevulinic acid (5-ALA), which can be synthesized by a single enzyme (5-ALA synthase or AlaS, Shemin pathway) or by a two-enzyme pathway. The genomes of some bacteriophages from aquatic environments carry various tetrapyrrole biosynthesis genes. Here, we analyze available metagenomic datasets and identify alaS homologs (viral alaS, or valaS) in sequences corresponding to marine and freshwater phages. The genes are found individually or as part of complete or truncated three-gene loci encoding heme-catabolizing enzymes. Amino-acid sequence alignments and three-dimensional structure prediction support that the valaS sequences likely encode functional enzymes. Indeed, we demonstrate that is the case for a freshwater phage valaS sequence, as it can complement an Escherichia coli 5-ALA auxotroph, and an E. coli strain overexpressing the gene converts the typical AlaS substrates glycine and succinyl-CoA into 5-ALA. Thus, our work identifies valaS as an auxiliary metabolic gene in phage sequences from aquatic environments, further supporting the importance of tetrapyrrole metabolism in bacteriophage biology.},
}
@article {pmid39406574,
year = {2024},
author = {Steinberg, R and Moeller, A and Gisler, A and Mostacci, N and Hilty, M and Usemann, J},
title = {Longitudinal effects of elexacaftor/tezacaftor/ivacaftor on the oropharyngeal metagenome in adolescents with cystic fibrosis.},
journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jcf.2024.10.001},
pmid = {39406574},
issn = {1873-5010},
abstract = {BACKGROUND: Triple modulator therapy elexacaftor/tezacaftor/ivacaftor (ETI) improves lung function and impacts upon the respiratory microbiome in people with Cystic fibrosis (pwCF) with advanced lung disease. However, adolescents with cystic fibrosis (CF) are less colonized with bacterial pathogens than adult pwCF but their microbiota already differs from healthy individuals. The aim of this study was to longitudinally analyze the impact of ETI on the respiratory metagenome in adolescents with predominantly mild CF lung disease.<br><br>METHODS: In this prospective observational study, we included pwCF aged 12-20 years with at least one F508del mutation, who collected oropharyngeal swabs before and after initiation of ETI therapy twice per week to biweekly over three months. We performed whole metagenome shotgun sequencing, followed by host DNA filtering and taxonomic profiling. We used linear and additive mixed effects models adjusted for known confounders and corrected for multiple testing to study longitudinal development of the microbiome. We analyzed bacterial diversity, abundance, and strain-level phylogeny.<br><br>RESULTS: We analyzed the metagenomic data of 297 swabs of 20 pwCF. Microbiome composition changed after initiation of ETI therapy. We observed a slight diversification of the microbiome over time (Inv Simpson, Coef 0.085, 95 %CI 0.003, 0.17, p = 0.04). Strain-level analysis and clustering showed that strain retention of the most frequent bacterial species is predominant even during ETI therapy.<br><br>CONCLUSIONS: During three months of ETI therapy, commensal bacteria increased, which may help to prevent overgrowth of bacterial pathogens.},
}
@article {pmid39406541,
year = {2024},
author = {Liu, ZB and Zhang, F and Liang, CY and Chen, WH and Wang, YM and Cui, XJ and Zhao, L and Cao, B},
title = {[Clinical characteristics of 29 cases of pulmonary mucormycosis treated with and without surgery].},
journal = {Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and respiratory diseases},
volume = {47},
number = {10},
pages = {946-954},
doi = {10.3760/cma.j.cn112147-20240426-00223},
pmid = {39406541},
issn = {1001-0939},
support = {ZRJY2023-GG13//China-Japan Friendship Hospital "Elite Plan" Talents Training Project/ ; },
mesh = {Humans ; Male ; *Mucormycosis/diagnosis/therapy ; Female ; Middle Aged ; Retrospective Studies ; Aged ; *Lung Diseases, Fungal/diagnosis/drug therapy/microbiology ; Antifungal Agents/therapeutic use ; },
abstract = {Objective: To analyze the clinical characteristics of patients with pulmonary mucormycosis treated with and without surgery. Methods: This was a single-center, retrospective study. We retrieved "pulmonary mucormycosis" from the electronic medical records of China-Japan Friendship Hospital between 2016 and 2022. A total of 29 patients with pulmonary mucormycosis were collected. There were 19 males and 10 females with a median age of 49 (47, 67) years. Mann-Whitney U test, χ[2] test, Kaplan-Meier curve and log-rank test were used to compare the differences between groups. Results: The most common underlying disease was diabetes (19, 65.5%). The most frequent imaging findings were consolidation (25, 86.2%) and nodule or mass (21, 72.4%). Bronchial stenosis (16, 55.2%), obstruction by fungal plugs (18, 62.1%), pseudomembranous necrotizing bronchitis (19, 65.5%) were common. Treatment strategies were developed by the multi-disciplinary team (MDT). Among 16 patients who did not undergo surgery, 10 had bilateral multifocal lesions and 6 had unifocal lesions. All patients received antifungal therapies, and surgeries were performed in 13 (44.8%) patients. Patients who underwent surgery had numerically lower in-hospital mortality (15.4% vs. 31.3%, P=0.410). Involvement of unilateral multiple lesions was more common in patients who underwent surgeries (6/13 vs. 1/16, P=0.019). Patients who underwent surgery were more likely to have lobar and segmental bronchial involvement (13/13 vs. 9/16, P=0.007). A total of 15 patients underwent mNGS, 14 (93.3%) had positive results. Performing metagenomic next generation sequencing for diagnosis shortened the time from disease onset to diagnosis (log-rank P=0.014). Conclusion: Metagenomic next-generation sequencing aided early diagnosis. The patients who underwent surgery included unilateral multiple lesions and visualisation of endobronchial abnormalities on lobar or segmental bronchus in unilateral lung.},
}
@article {pmid39406503,
year = {2024},
author = {Valentin-Alvarado, LE and Shi, LD and Appler, KE and Crits-Christoph, A and De Anda, V and Adler, BA and Cui, ML and Ly, L and Leão, P and Roberts, RJ and Sachdeva, R and Baker, BJ and Savage, DF and Banfield, JF},
title = {Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.279480.124},
pmid = {39406503},
issn = {1549-5469},
abstract = {Asgard archaea are of great interest as the progenitors of Eukaryotes, but little is known about the mobile genetic elements (MGEs) that may shape their ongoing evolution. Here, we describe MGEs that replicate in Atabeyarchaeia, a wetland Asgard archaea lineage represented by two complete genomes. We used soil depth-resolved population metagenomic data sets to track 18 MGEs for which genome structures were defined and precise chromosome integration sites could be identified for confident host linkage. Additionally, we identified a complete 20.67 kbp circular plasmid and two family-level groups of viruses linked to Atabeyarchaeia, via CRISPR spacer targeting. Closely related 40 kbp viruses possess a hypervariable genomic region encoding combinations of specific genes for small cysteine-rich proteins structurally similar to restriction-homing endonucleases. One 10.9 kbp integrative conjugative element (ICE) integrates genomically into the Atabeyarchaeum deiterrae-1 chromosome and has a 2.5 kbp circularizable element integrated within it. The 10.9 kbp ICE encodes an expressed Type IIG restriction-modification system with a sequence specificity matching an active methylation motif identified by Pacific Biosciences (PacBio) high-accuracy long-read (HiFi) metagenomic sequencing. Restriction-modification of Atabeyarchaeia differs from that of another coexisting Asgard archaea, Freyarchaeia, which has few identified MGEs but possesses diverse defense mechanisms, including DISARM and Hachiman, not found in Atabeyarchaeia. Overall, defense systems and methylation mechanisms of Asgard archaea likely modulate their interactions with MGEs, and integration/excision and copy number variation of MGEs in turn enable host genetic versatility.},
}
@article {pmid39406043,
year = {2024},
author = {Lv, J and Liu, C and Fan, L and Luo, P and Liu, S and Wu, C},
title = {Omadacycline for the treatment of severe Legionella pneumophila pneumonia complicated with multiple organ dysfunction: a case report.},
journal = {Diagnostic microbiology and infectious disease},
volume = {110},
number = {4},
pages = {116553},
doi = {10.1016/j.diagmicrobio.2024.116553},
pmid = {39406043},
issn = {1879-0070},
abstract = {Omadacycline is a novel tetracycline antibiotic that has a strong in vitro antibacterial activity against atypical pathogen such as Legionella. It is approved for the treatment of adults with community-acquired bacterial pneumonia, including Legionella pneumonia. However, clinical data on the use of omadacycline in Legionella pneumonia is limited. In the present paper, we report a case of severe pneumonia induced by Legionella pneumophila (L.pneumophila) presenting with septic shock and multiple organ dysfunction including lung, liver and kidney. With omadacycline treaetment, inflammation indices of the patient markedly decreased, and the patient significantly improved with multiple organ dysfunction and was discharged from home. Due to its strong antibacterial activity against L.pneumophila, good safety profile and no dosage adjustment in patients with severe hepatic or renal impairment, omadacycline can be considered as an optimal treatment strategies for severe infections by such special pathogen. Whereas, more case reports are needed to support this conclusion.},
}
@article {pmid39405960,
year = {2024},
author = {Cheng, H and Zhang, ZY and Han, H and Wei, R and Zhao, W and Sun, YC and Xu, BB and Hou, XL and Wang, JL and He, YQ and Fu, Y and Wang, QS and Pan, YC and Zhang, Z and Wang, Z},
title = {Cross-ancestry meta-genome-wide association studies provide insights to the understanding of semen traits in pigs.},
journal = {Animal : an international journal of animal bioscience},
volume = {18},
number = {11},
pages = {101331},
doi = {10.1016/j.animal.2024.101331},
pmid = {39405960},
issn = {1751-732X},
abstract = {Semen traits play a crucial role in pig reproduction and fertility. However, limited data availability hinder a comprehensive understanding of the genetic mechanisms underlying these traits. In this study, we integrated 597 299 ejaculates and 3 596 sequence data to identify genetic variants and candidate genes related to four semen traits, including sperm progressive motility (MOT), semen volume, sperm concentration (CON), and effective sperm count (SUM). A cross-ancestry meta-genome-wide association study was conducted to detect 163 lead single nucleotide polymorphisms (SNPs) associated with MOT, CON, and SUM. Subsequently, transcriptome-wide association studies and colocalisation analyses were integrated to identify 176 candidate genes, many of which have documented roles in spermatogenesis or male mammal semen traits. Our analysis highlighted the potential involvement of CSM5, PDZD9, and LDAF1 in regulating semen traits through multiple methods. Finally, to validate the function of significant SNPs, we performed genomic feature best linear unbiased prediction in 348 independent pigs using identified trait-related SNP subsets as genomic features. We found that integrating the top 0.1, 1, and 5% significant SNPs as genomic features could enhance genomic prediction accuracy for CON and MOT compared to traditional genomic best linear unbiased prediction. This study contributes to a comprehensive understanding of the genetic mechanisms of boar semen traits and provides insight for developing genomic selection models.},
}
@article {pmid39405850,
year = {2024},
author = {Liu, Y and Wen, M and Hu, R and Zhao, F and Wang, J},
title = {Regulation of wheat yield by soil multifunctionality and metagenomic-based microbial degradation potentials under crop rotations.},
journal = {Journal of environmental management},
volume = {370},
number = {},
pages = {122897},
doi = {10.1016/j.jenvman.2024.122897},
pmid = {39405850},
issn = {1095-8630},
abstract = {Crop rotation benefits soil fertility and crop yield by providing organic components including cellulose, lignin, chitin, and glucans that are mainly degraded by soil microbial carbohydrate-active enzymes (CAZymes). However, the impacts of crop rotation on soil microbial CAZyme genes are not well understood. Hence, CAZyme genes and families involved in the degradation of differentially originated organic components were investigated using metagenomics among distinct crop rotations. Crop rotation had a more significant effect on soil nitrogen than on carbon fractions with higher content in the complex rotation referring to alfalfa (Medicago sativa L.; 4 year)-potato (Solanum tuberosum L.; 1 year)-winter wheat (3 year; A4PoW3). The composition of soil microbial CAZyme genes related to the degradation of fungi-derived components was more affected by crop rotation compared with the degradation of plant- and bacteria-derived components. The total abundance of CAZyme genes and families was significantly higher in the complex rotation. Notably, CAZyme genes belonging to glycoside hydrolase and glycosyl transferase families had more connections in their network. Moreover, key genes including CE4, GH20, and GH23 assembled toward the middle of the network, and were significantly regulated by dominant soil nitrogen fractions including soil potential nitrogen mineralization and microbial biomass nitrogen. Soil multifunctionality was mostly explained by the composition and total abundance of CAZyme genes, but wheat grain yield was profoundly regulated by fungi-derived components degradation genes under effects of dominant nitrogen fractions. Overall, the findings provide deep insight into the degradation potentials of soil microbial CAZyme genes for developing sustainable crop rotational agroecosystems.},
}
@article {pmid39405720,
year = {2024},
author = {He, Y and Li, Y and Pan, Y and Shang, J and Sun, W and Wang, M and Fan, H and Sanford, RA and Wei, N and Peng, S and Xie, D and Zhang, W and Chen, S and Liu, Y and Jiang, Z and Jiang, Y and Hu, Y and Li, S and Hu, N and Dong, Y and Shi, L},
title = {Intimate microbe-water-mineral interactions mediate alkalization in the pyroxene-rich iron ore mines in Panxi area, Southwest China.},
journal = {Journal of hazardous materials},
volume = {480},
number = {},
pages = {136127},
doi = {10.1016/j.jhazmat.2024.136127},
pmid = {39405720},
issn = {1873-3336},
abstract = {In contrast to acid mine drainage, the microbial assembly and (bio)geochemical processes in alkaline mine conditions remain under-investigated. Here, microbe-water-mineral interactions were systematically investigated in two representative iron mines with alkaline conditions in the Panxi mining area, Southwest China. Compared to reference riverine samples less interfered by mining activities, the iron ore samples, composed of vanadium-titanium magnetite and pyroxene-rich bedrocks, exhibited elevated levels of Fe, HCl-extractable Fe(II), total sulfur, nitrate and sulfate, but lower total carbon (TC). Meanwhile, the mine drainage showed significantly higher sulfate, but lower TC concentrations than the riverine samples. Intriguingly, the Serpentinimonas spp., typically reported in serpentinites, prevailed in the microbial communities from the mine samples exhibiting higher pH. This suggests that the alkaline environments in Panxi mines result from serpentinization-like reactions. Enrichment of Thiobacillus spp. was observed in the mine-dwelling microbial communities, positively correlated with total sulfur, sulfate, nitrate, and Fe(II). Genome-resolved metagenomics suggested a chemoautotrophic lifestyle for the Thiobacillus species (e.g., carbon fixation, sulfur oxidation, and oxygen respiration), which may generate H[+] and mitigate alkalization. This study provides valuable insights into progressive development of alkaline mine ecosystems and offers guidance for developing appropriate engineering strategies to restore the abandoned alkaline mines.},
}
@article {pmid39405686,
year = {2024},
author = {Zhang, S and Hou, R and Wang, Y and Huang, Q and Lin, L and Li, H and Liu, S and Jiang, Z and Huang, X and Xu, X},
title = {Xenobiotic metabolism activity of gut microbiota from six marine species: Combined taxonomic, metagenomic, and in vitro transformation analysis.},
journal = {Journal of hazardous materials},
volume = {480},
number = {},
pages = {136152},
doi = {10.1016/j.jhazmat.2024.136152},
pmid = {39405686},
issn = {1873-3336},
abstract = {The xenobiotic metabolism driven by the gut microbiota significantly regulates the bioavailability and toxic effects of environmental pollutants such as plasticizers on aquatic organisms. However, it is still unknown whether the gut microbiota can exhibit variable metabolic ability across host species and which functional bacteria and genes are involved in xenobiotic transformation. This study investigated the enriched gut microbiota community composition and diversity of in vitro enrichment cultures from 6 marine species, namely, yellowfin seabream (Acanthopagrus latus), thorn fish (Terapon jarbua), shortnose ponyfish (Leiognathus brevirostris), mussel (Perna viridis), prawn (Parapenaeopsis hungerfordi) and crab (Charybdis riversandersoni). Pseudomonadota, Bacteroidota and Bacillota were the dominant phyla and Enterobacter, Raoultella, Klebsiella, Dysgonomanas and Lactococcus were the dominant genera in the enriched flora according to 16S rRNA sequencing. Furthermore, the metagenomic results revealed that all enriched gut microbiota presented metabolic genes for carbohydrates, amino acids, lipids, and xenobiotics. In particular, the gut microbiota of yellowfin seabream had the highest abundance of glycoside hydrolase family genes and CYP450 enzyme genes. Klebsiella was identified as a common potential degrader of xenobiotic metabolism. In addition, the Biolog plate test system confirmed that the gut microbiota can metabolize various carbon sources and drive the xenobiotic transformation. According to AWCD analysis of community level physiological profiling (CLPP), yellowfin seabream > mussel > prawn > shortnose ponyfish > crab > thorn fish. The gut microbiota of yellowfin seabream presented a stronger metabolic profile of phthalates and bisphenol analogs which reflected by their AWCD results and concentration variations. Overall, our results demonstrated the diverse metabolic abilities of the gut microbiota from six marine organisms and their potential for altering of the fate of xenobiotics in the ecosystem on the basis of combined taxonomic, metagenomic, and in vitro transformation analysis.},
}
@article {pmid39405675,
year = {2024},
author = {Xing, BS and Su, YM and Fu, YL and Wu, YF and Yan, CH and Wang, XC and Li, YY and Chen, R},
title = {Comparison of the short- and long-term effects of zinc ions on the anaerobic mesophilic co-digestion of food waste and waste activated sludge: Digester performance, antibiotic resistance gene reduction and the microbial community.},
journal = {Journal of hazardous materials},
volume = {480},
number = {},
pages = {136119},
doi = {10.1016/j.jhazmat.2024.136119},
pmid = {39405675},
issn = {1873-3336},
abstract = {Heavy metals contained in waste activated sludge (WAS), especially zinc ions, have an inhibitory effect on the anaerobic digestion. However, the effects of zinc ions on digester performance, antibiotic resistance genes (ARGs) reduction, and the microbial community involved in the anaerobic mesophilic co-digestion (AcoD) of WAS and food waste (FW) have not been fully characterized. Therefore, batch trials and continuous stirred tank reactors were used under different zinc-ion concentrations. Findings showed that the AcoD system can tolerate a maximum zinc ion of 540 mg/L in a short-term batch and 470 mg/L in a long-term AcoD system, promoting methane production of approximately 1.0-17.0 %. Metagenomic analysis revealed that syntrophic H2 transfer occurred between Syntrophomonas and Methanoculleus and the aceticlastic and hydrogenotrophic methanogenic pathways were both enhanced by 1.18- and 1.16 times, respectively. Moreover, the relative abundance of Methanosarcina increased from 58.4 % to 72.5 % at 470 mg/L to adapt to the high zinc ion concentration during long-term continuous operation. These results revealed that AcoD with a low zinc ion concentration can effectively increase the removal percentage of ARGs. The results provide guidance for biogas recovery and use of mesophilic AcoD with FW and WAS containing high zinc ion concentrations without pretreatment process.},
}
@article {pmid39405634,
year = {2024},
author = {Leijonhufvud, G and Soratto, TAT and Matos, GM and Bajalan, A and Eichler-Jonsson, C and Gustafsson, B and Bogdanovic, G and Allander, T and Ljungman, G and Andersson, B},
title = {Metagenomic characterization of viruses in the serum of children with newly diagnosed cancer.},
journal = {Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology},
volume = {175},
number = {},
pages = {105736},
doi = {10.1016/j.jcv.2024.105736},
pmid = {39405634},
issn = {1873-5967},
abstract = {BACKGROUND AND OBJECTIVES: A large cohort of pediatric patients with various forms of childhood cancer was investigated for the presence of viruses using metagenomics. A total of 476 patient samples, collected between 1989 and 2018, were analyzed, representing various pediatric oncological diagnoses and a control group of non-malignant diagnoses.<br><br>STUDY DESIGN: The study was carried out using metagenomic sequencing of serum samples. Viruses were identified and analyzed using bioinformatics methods, followed by Polymerase chain reaction (PCR) confirmation RESULTS: The results indicate that a wide range of viruses can be detected in the bloodstream of children with newly diagnosed cancer. Nine viral genomes were identified: Human Pegivirus (HPgV), Hepatitis C virus, Parechovirus 1, Rhinovirus C, Human papillomavirus 116, Human polyomavirus 10, Parvovirus B19, and different variants of Torque Teno Virus (TTV). In this study, a previously unknown virus was found belonging to the Iflavirdae family in the order Picornavirales. HPGV was significantly more common in patients with leukemia compared to other conditions.<br><br>CONCLUSIONS: These results highlight the abundance of systemic virus infections in children, and the value of metagenomic sequencing for hypothesis forming regarding the associations between virus infections and cancer.},
}
@article {pmid39405631,
year = {2024},
author = {Guruge, SK and Han, Z and Dai, S and Islam, A and Ben, W and Tian, Z and Zhang, Y and Yang, M},
title = {Seasonal variation of antibiotic resistance genes in activated sludge of a full-scale municipal wastewater treatment plant: Contribution of activated sludge functional taxa and clinically relevant taxa.},
journal = {Water research},
volume = {268},
number = {Pt A},
pages = {122598},
doi = {10.1016/j.watres.2024.122598},
pmid = {39405631},
issn = {1879-2448},
abstract = {It has been demonstrated that antibiotic resistance genes (ARGs) exhibit seasonal variations in municipal wastewater treatment plants (MWTPs), but their relationship to bacterial phylogeny structure remains unclear. Using advanced metagenomic techniques and machine learning approach, the current study conducted a year-long investigation to explore the relationship between ARGs and the bacterial community of activated sludge in a full-scale MWTP in Beijing, where seasonal dynamics are remarkable. High abundance of ARGs, notably the clinically relevant high-risk ARGs, was observed in winter and spring, the cold season in Beijing. Seasonal patterns were also observed in the diversity of ARGs and the overall bacterial community. Machine learning-based random forest classification models were utilized to identify biomarkers for ARGs and bacterial genera as indicators of seasonal differences. Subsequent analysis of the relationship between ARGs and bacterial biomarkers was examined using random forest regression models. Results showed that the enrichment of potential pathogens such as Mycobacterium, Clostridium and Pseudomonas was high in winter and spring, strongly contributing to the abundance of high-risk ARGs (ermB, aac(6')-I, tetM, blaTEM, and mefA) during cold season. Conversely, functional taxa associated with activated sludge, such as Thauera, displayed seasonal fluctuations and a preference for ARGs with minor clinical implications. Metagenomic binning further illustrated the contribution of Mycobacterium to ARG enrichment in cold season. Our findings highlight the collective impact of human-derived clinically relevant taxa and functional bacterial taxa in activated sludge on the seasonal dynamics of ARGs in MWTPs. Additionally, this study offers valuable insights into the safe disposal of the excess sludge from MWTPs.},
}
@article {pmid39405475,
year = {2024},
author = {Rodríguez-Pérez, H and Ciuffreda, L and Hernández-Beeftink, T and Guillen-Guio, B and Domínguez, D and Corrales, A and Espinosa, E and Alcoba-Florez, J and Lorenzo-Salazar, JM and González-Montelongo, R and Villar, J and Flores, C},
title = {Tracheal Aspirate Metagenomics Reveals Association of Antibiotic Resistance with Non-Pulmonary Sepsis Mortality.},
journal = {American journal of respiratory cell and molecular biology},
volume = {},
number = {},
pages = {},
doi = {10.1165/rcmb.2024-0192LE},
pmid = {39405475},
issn = {1535-4989},
}
@article {pmid39404832,
year = {2024},
author = {Díaz-Martínez, C and Bolívar, A and Mercanoglu Taban, B and Kanca, N and Pérez-Rodríguez, F},
title = {Exploring the antibiotic resistance of Listeria monocytogenes in food environments - a review.},
journal = {Critical reviews in microbiology},
volume = {},
number = {},
pages = {1-24},
doi = {10.1080/1040841X.2024.2412007},
pmid = {39404832},
issn = {1549-7828},
abstract = {Listeria monocytogenes, a resilient bacterium in diverse food conditions, such as refrigeration, reduced water activity and low pH, poses a significant threat to the food industry and public health. In recent years, it has been documented an increase in the antibiotic resistance of zoonotic pathogens, including L. monocytogenes. This review provides new insight into the molecular mechanisms involved in both intrinsic and acquired antibiotic resistance of L. monocytogenes with an emphasis on the effect of different environmental and food-related factors. It also explores the relationship of these resistance mechanisms with virulence factors. An analysis of literature data (2009-2021) was conducted to investigate statistically and graphically potential associations between specific antibiotic resistance patterns in the pathogen and food categories using an unbiased variance analysis. The results evidenced that food type had an influence on the antibiotic resistance profiles of L. monocytogenes, with meat and vegetables being the food categories exhibiting the most prevalent profiles. The frequent detection of resistance to ampicillin, penicillin, and tetracycline (non-intrinsic resistances) indicates that specific processing conditions along the food chain may induce them. Many questions remain about the impact of food chain factors (e.g. thermal treatments, cold chain, preservatives, etc.) and food type (low pH, reduced water activity, etc.) on the antibiotic resistance patterns of the pathogen, particularly concerning food-related sources, the resistance mechanisms involved (e.g. cross-protection, horizontal gene transfer, etc.), and the evolutionary processes of antibiotic-resistant microbial populations. Metagenomics, in addition to other -omics technologies (metabolomics and transcriptomics), allows a better understanding of the processes involved in the acquisition of resistance.},
}
@article {pmid39404267,
year = {2024},
author = {Olie, SE and Andersen, C&#xd8; and van de Beek, D and Brouwer, MC},
title = {Molecular diagnostics in cerebrospinal fluid for the diagnosis of central nervous system infections.},
journal = {Clinical microbiology reviews},
volume = {},
number = {},
pages = {e0002124},
doi = {10.1128/cmr.00021-24},
pmid = {39404267},
issn = {1098-6618},
abstract = {SUMMARYCentral nervous system (CNS) infections can be caused by various pathogens, including bacteria, viruses, fungi, and parasites. Molecular diagnostic methods are pivotal for identifying the different causative pathogens of these infections in clinical settings. The efficacy and specificity of these methods can vary per pathogen involved, and in a substantial part of patients, no pathogen is identified in the cerebrospinal fluid (CSF). Over recent decades, various molecular methodologies have been developed and applied to patients with CNS infections. This review provides an overview of the accuracy of nucleic acid amplification methods in CSF for a diverse range of pathogens, examines the potential value of multiplex PCR panels, and explores the broad-range bacterial and fungal PCR/sequencing panels. In addition, it evaluates innovative molecular approaches to enhance the diagnosis of CNS infections.},
}
@article {pmid39404262,
year = {2024},
author = {Zhong, C and Yamanouchi, S and Li, Y and Chen, J and Wei, T and Wang, R and Zhou, K and Cheng, A and Hao, W and Liu, H and Konhauser, KO and Iwasaki, W and Qian, P-Y},
title = {Marine biofilms: cyanobacteria factories for the global oceans.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0031724},
doi = {10.1128/msystems.00317-24},
pmid = {39404262},
issn = {2379-5077},
abstract = {UNLABELLED: Marine biofilms were newly revealed as a giant microbial diversity pool for global oceans. However, the cyanobacterial diversity in marine biofilms within the upper seawater column and its ecological and evolutionary implications remains undetermined. Here, we reconstructed a full picture of modern marine cyanobacteria habitats by re-analyzing 9.3 terabyte metagenomic data sets and 2,648 metagenome-assembled genomes (MAGs). The abundances of cyanobacteria lineages exclusively detected in marine biofilms were up to ninefold higher than those in seawater at similar sample size. Analyses revealed that cyanobacteria in marine biofilms are specialists with strong geographical and environmental constraints on their genome and functional adaption, which is in stark contrast to the generalistic features of seawater-derived cyanobacteria. Molecular dating suggests that the important diversifications in biofilm-forming cyanobacteria appear to coincide with the Great Oxidation Event (GOE), "boring billion" middle Proterozoic, and the Neoproterozoic Oxidation Event (NOE). These new insights suggest that marine biofilms are large and important cyanobacterial factories for the global oceans.<br><br>IMPORTANCE: Cyanobacteria, highly diverse microbial organisms, play a crucial role in Earth's oxygenation and biogeochemical cycling. However, their connection to these processes remains unclear, partly due to incomplete surveys of oceanic niches. Our study uncovered significant cyanobacterial diversity in marine biofilms, showing distinct niche differentiation compared to seawater counterparts. These patterns reflect three key stages of marine cyanobacterial diversification, coinciding with major geological events in the Earth's history.},
}
@article {pmid39402695,
year = {2024},
author = {Nawaz, MA and Pamirsky, IE and Golokhvast, KS},
title = {Bioinformatics in Russia: history and present-day landscape.},
journal = {Briefings in bioinformatics},
volume = {25},
number = {6},
pages = {},
doi = {10.1093/bib/bbae513},
pmid = {39402695},
issn = {1477-4054},
support = {075-15-2022-1152/7//Ministry of Science and Higher Education of the Russian Federation to Advanced Engineering School/ ; //National Research State University, Tomsk, Russia/ ; 20-53-56041//Russian Foundation for Basic Research/ ; },
mesh = {*Computational Biology/methods ; Russia ; Humans ; History, 21st Century ; History, 20th Century ; Genomics ; },
abstract = {Bioinformatics has become an interdisciplinary subject due to its universal role in molecular biology research. The current status of Russia's bioinformatics research in Russia is not known. Here, we review the history of bioinformatics in Russia, present the current landscape, and highlight future directions and challenges. Bioinformatics research in Russia is driven by four major industries: information technology, pharmaceuticals, biotechnology, and agriculture. Over the past three decades, despite a delayed start, the field has gained momentum, especially in protein and nucleic acid research. Dedicated and shared centers for genomics, proteomics, and bioinformatics are active in different regions of Russia. Present-day bioinformatics in Russia is characterized by research issues related to genetics, metagenomics, OMICs, medical informatics, computational biology, environmental informatics, and structural bioinformatics. Notable developments are in the fields of software (tools, algorithms, and pipelines), use of high computation power (e.g. by the Siberian Supercomputer Center), and large-scale sequencing projects (the sequencing of 100 000 human genomes). Government funding is increasing, policies are being changed, and a National Genomic Information Database is being established. An increased focus on eukaryotic genome sequencing, the development of a common place for developers and researchers to share tools and data, and the use of biological modeling, machine learning, and biostatistics are key areas for future focus. Universities and research institutes have started to implement bioinformatics modules. A critical mass of bioinformaticians is essential to catch up with the global pace in the discipline.},
}
@article {pmid39402664,
year = {2024},
author = {Ndiaye, M and Prieto-Baños, S and Fitzgerald, LM and Yazdizadeh Kharrazi, A and Oreshkov, S and Dessimoz, C and Sedlazeck, FJ and Glover, N and Majidian, S},
title = {When less is more: sketching with minimizers in genomics.},
journal = {Genome biology},
volume = {25},
number = {1},
pages = {270},
pmid = {39402664},
issn = {1474-760X},
abstract = {The exponential increase in sequencing data calls for conceptual and computational advances to extract useful biological insights. One such advance, minimizers, allows for reducing the quantity of data handled while maintaining some of its key properties. We provide a basic introduction to minimizers, cover recent methodological developments, and review the diverse applications of minimizers to analyze genomic data, including de novo genome assembly, metagenomics, read alignment, read correction, and pangenomes. We also touch on alternative data sketching techniques including universal hitting sets, syncmers, or strobemers. Minimizers and their alternatives have rapidly become indispensable tools for handling vast amounts of data.},
}
@article {pmid39402510,
year = {2024},
author = {Abramova, A and Karkman, A and Bengtsson-Palme, J},
title = {Metagenomic assemblies tend to break around antibiotic resistance genes.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {959},
pmid = {39402510},
issn = {1471-2164},
abstract = {BACKGROUND: Assembly of metagenomic samples can provide essential information about the mobility potential and taxonomic origin of antibiotic resistance genes (ARGs) and inform interventions to prevent further spread of resistant bacteria. However, similar to other conserved regions, such as ribosomal RNA genes and mobile genetic elements, almost identical ARGs typically occur in multiple genomic contexts across different species, representing a considerable challenge for the assembly process. Usually, this results in many fragmented contigs of unclear origin, complicating the risk assessment of ARG detections. To systematically investigate the impact of this issue on detection, quantification and contextualization of ARGs, we evaluated the performance of different assembly approaches, including genomic-, metagenomic- and transcriptomic-specialized assemblers. We quantified recovery and accuracy rates of each tool for ARGs both from in silico spiked metagenomic samples as well as real samples sequenced using both long- and short-read sequencing technologies.<br><br>RESULTS: The results revealed that none of the investigated tools can accurately capture genomic contexts present in samples of high complexity. The transcriptomic assembler Trinity showed a better performance in terms of reconstructing longer and fewer contigs matching unique genomic contexts, which can be beneficial for deciphering the taxonomic origin of ARGs. The currently commonly used metagenomic assembly tools metaSPAdes and MEGAHIT were able to identify the ARG repertoire but failed to fully recover the diversity of genomic contexts present in a sample. On top of that, in a complex scenario MEGAHIT produced very short contigs, which can lead to considerable underestimation of the resistome in a given sample.<br><br>CONCLUSIONS: Our study shows that metaSPAdes and Trinity would be the preferable tools in terms of accuracy to recover correct genomic contexts around ARGs in metagenomic samples characterized by uneven coverages. Overall, the inability of assemblers to reconstruct long ARG-containing contigs has impacts on ARG quantification, suggesting that directly mapping reads to an ARG database should be performed as a complementary strategy to get accurate ARG abundance and diversity measures.},
}
@article {pmid39402441,
year = {2024},
author = {Yang, M and Wang, Z and Yan, Z and Wang, W and Zhu, Q and Jin, C},
title = {DNASimCLR: a contrastive learning-based deep learning approach for gene sequence data classification.},
journal = {BMC bioinformatics},
volume = {25},
number = {1},
pages = {328},
pmid = {39402441},
issn = {1471-2105},
abstract = {BACKGROUND: The rapid advancements in deep neural network models have significantly enhanced the ability to extract features from microbial sequence data, which is critical for addressing biological challenges. However, the scarcity and complexity of labeled microbial data pose substantial difficulties for supervised learning approaches. To address these issues, we propose DNASimCLR, an unsupervised framework designed for efficient gene sequence data feature extraction.<br><br>RESULTS: DNASimCLR leverages convolutional neural networks and the SimCLR framework, based on contrastive learning, to extract intricate features from diverse microbial gene sequences. Pre-training was conducted on two classic large scale unlabelled datasets encompassing metagenomes and viral gene sequences. Subsequent classification tasks were performed by fine-tuning the pretrained model using the previously acquired model. Our experiments demonstrate that DNASimCLR is at least comparable to state-of-the-art techniques for gene sequence classification. For convolutional neural network-based approaches, DNASimCLR surpasses the latest existing methods, clearly establishing its superiority over the state-of-the-art CNN-based feature extraction techniques. Furthermore, the model exhibits superior performance across diverse tasks in analyzing biological sequence data, showcasing its robust adaptability.<br><br>CONCLUSIONS: DNASimCLR represents a robust and database-agnostic solution for gene sequence classification. Its versatility allows it to perform well in scenarios involving novel or previously unseen gene sequences, making it a valuable tool for diverse applications in genomics.},
}
@article {pmid39402236,
year = {2024},
author = {Vera-Ponce de León, A and Hensen, T and Hoetzinger, M and Gupta, S and Weston, B and Johnsen, SM and Rasmussen, JA and Clausen, CG and Pless, L and Veríssimo, ARA and Rudi, K and Snipen, L and Karlsen, CR and Limborg, MT and Bertilsson, S and Thiele, I and Hvidsten, TR and Sandve, SR and Pope, PB and La Rosa, SL},
title = {Genomic and functional characterization of the Atlantic salmon gut microbiome in relation to nutrition and health.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {39402236},
issn = {2058-5276},
support = {300846//Norges Forskningsr&#xe5;d (Research Council of Norway)/ ; 757922//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 12/RC/2273-P2//Science Foundation Ireland (SFI)/ ; },
abstract = {To ensure sustainable aquaculture, it is essential to understand the path 'from feed to fish', whereby the gut microbiome plays an important role in digestion and metabolism, ultimately influencing host health and growth. Previous work has reported the taxonomic composition of the Atlantic salmon (Salmo salar) gut microbiome; however, functional insights are lacking. Here we present the Salmon Microbial Genome Atlas consisting of 211 high-quality bacterial genomes, recovered by cultivation (n = 131) and gut metagenomics (n = 80) from wild and farmed fish both in freshwater and seawater. Bacterial genomes were taxonomically assigned to 14 different orders, including 35 distinctive genera and 29 previously undescribed species. Using metatranscriptomics, we functionally characterized key bacterial populations, across five phyla, in the salmon gut. This included the ability to degrade diet-derived fibres and release vitamins and other exometabolites with known beneficial effects, which was supported by genome-scale metabolic modelling and in vitro cultivation of selected bacterial species coupled with untargeted metabolomic studies. Together, the Salmon Microbial Genome Atlas provides a genomic and functional resource to enable future studies on salmon nutrition and health.},
}
@article {pmid39401075,
year = {2024},
author = {Oppermann, J and Rozenberg, A and Fabrin, T and González-Cabrera, C and Parker, R and Béjà, O and Prigge, M and Hegemann, P},
title = {Robust optogenetic inhibition with red-light-sensitive anion-conducting channelrhodopsins.},
journal = {eLife},
volume = {12},
number = {},
pages = {},
doi = {10.7554/eLife.90100},
pmid = {39401075},
issn = {2050-084X},
support = {SFB 1078 B2 221545957//Deutsche Forschungsgemeinschaft/ ; 3131/20//Israel Science Foundation/ ; 99999.001756/2014-01//Alexander von Humboldt-Stiftung/ ; JPco-FuND - NiPARK//EU Joint Programme - Neurodegenerative Disease Research/ ; Program 'BestMinds' MP J28/2017 SheLi//Leibniz-Gemeinschaft/ ; ASAP-020505//Aligning Science Across Parkinson's/ ; },
mesh = {*Optogenetics/methods ; Animals ; *Channelrhodopsins/genetics/metabolism ; Mice ; *Light ; *Neurons/metabolism/physiology/radiation effects ; Anions/metabolism ; Phylogeny ; Humans ; },
abstract = {Channelrhodopsins (ChRs) are light-gated ion channels widely used to optically activate or silence selected electrogenic cells, such as individual brain neurons. Here, we describe identifying and characterizing a set of anion-conducting ChRs (ACRs) from diverse taxa and representing various branches of the ChR phylogenetic tree. The Mantoniella squamata ACR (MsACR1) showed high sensitivity to yellow-green light (λmax at 555 nm) and was further engineered for optogenetic applications. A single amino-acid substitution that mimicked red-light-sensitive rhodopsins like Chrimson shifted the photosensitivity 20 nm toward red light and accelerated photocurrent kinetics. Hence, it was named red and accelerated ACR, raACR. Both wild-type and mutant are capable optical silencers at low light intensities in mouse neurons in vitro and in vivo, while raACR offers a higher temporal resolution.},
}
@article {pmid39400741,
year = {2024},
author = {Lemieux-Labonté, V and Pathmanathan, JS and Terrat, Y and Tromas, N and Simard, A and Haase, CG and Lausen, CL and Willis, CKR and Lapointe, FJ},
title = {Pseudogymnoascus destructans invasion stage impacts the skin microbial functions of highly vulnerable Myotis lucifugus.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiae138},
pmid = {39400741},
issn = {1574-6941},
abstract = {The role of the skin microbiome in resistance and susceptibility of wildlife to fungal pathogens has been examined from a taxonomic perspective but skin microbial function, in the context of fungal infection, has yet to be studied. Our objective was to understand effects of a bat fungal pathogen site infection status and course of invasion on skin microbial function. We sampled seven hibernating colonies of Myotis lucifugus covering three-time points over the course of Pseudogymnoascus destructans (Pd) invasion and white nose syndrome (pre-invasion, epidemic and established). Our results support three new hypotheses about Pd and skin functional microbiome: 1) there is an important effect of Pd invasion stage, especially at the epidemic stage; 2) disruption by the fungus at the epidemic stage could decrease anti-fungal functions with potential negative effects on the microbiome and bat health; 3) the collection site might have a larger influence on microbiomes at the pre-invasion stage rather than at epidemic and established stages. Future studies with larger samples size and using meta-omics approaches will help confirm these hypotheses, and determine the influence of the microbiome on wildlife survival to fungal disease.},
}
@article {pmid39400154,
year = {2024},
author = {Takemae, N and Kuba, Y and Oba, K and Kageyama, T},
title = {Direct genome sequencing of respiratory viruses from low viral load clinical specimens using the target capture sequencing technology.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0098624},
doi = {10.1128/spectrum.00986-24},
pmid = {39400154},
issn = {2165-0497},
abstract = {The use of metagenomic next-generation sequencing technology to obtain complete viral genome sequences directly from clinical samples with low viral load remains challenging-especially in the case of respiratory viruses-due to the low copy number of viral versus host genomes. To overcome this limitation, target capture sequencing for the enrichment of specific genomes has been developed and applied for direct genome sequencing of viruses. However, as the efficiency of enrichment varies depending on the probes, the type of clinical sample, etc., validation is essential before target capture sequencing can be applied to clinical diagnostics. In this study, we evaluated the utility of target capture sequencing with a comprehensive viral probe panel for clinical respiratory specimens collected from patients diagnosed with SARS-CoV-2 or influenza type A. We focused on clinical specimens containing low copy numbers of viral genomes. Target capture sequencing yielded approximately 180- and 2,000-fold higher read counts of SARS-CoV-2 and influenza A virus, respectively, than metagenomic sequencing when the RNA extracted from specimens contained 59.3 copies/µL of SARS-CoV-2 or 625.1 copies/µL of influenza A virus. In addition, the target capture sequencing identified sequence reads in all SARS-CoV-2- or influenza type A-positive specimens with <26 RNA copies/µL, some of which also yielded >70% of the full-length genomes of SARS-CoV-2 or influenza A virus. Furthermore, the target capture sequencing using comprehensive probes identified co-infections with viruses other than SARS-CoV-2, suggesting that this approach will not only detect a wide range of viruses but also contribute to epidemiological studies.IMPORTANCETarget capture sequencing has been developed and applied for direct genome sequencing of viruses in clinical specimens to overcome the low detection sensitivity of metagenomic next-generation sequencing. In this study, we evaluated the utility of target capture sequencing with a comprehensive viral probe panel for clinical respiratory specimens collected from patients diagnosed with SARS-CoV-2 or influenza type A, focusing on clinical specimens containing low copy numbers of viral genomes. Our results showed that the target capture sequencing yielded dramatically higher read counts than metagenomic sequencing for both viruses. Furthermore, the target capture sequencing using comprehensive probes identified co-infections with other viruses, suggesting that this approach will not only detect a wide range of viruses but also contribute to epidemiological studies.},
}
@article {pmid39400140,
year = {2024},
author = {Laureano, G and Bermudez, AE and Rivera Vicéns, RE and Arun, A},
title = {Metagenome-assembled genome of Pseudomonas sp. from coenocytic alga Vaucheria bursata.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0048524},
doi = {10.1128/mra.00485-24},
pmid = {39400140},
issn = {2576-098X},
abstract = {Here, we report a draft metagenome-assembled genome and annotation of Pseudomonas sp. obtained from the sequenced genome of Vaucheria bursata. The genome completeness was 97.9% with a total of 5,322 open reading frames, of which 3,147 genes were annotated. The availability of the metagenome will elucidate the possible epiphytic interactions of bacteria with Vaucheria bursata.},
}
@article {pmid39399973,
year = {2024},
author = {Simpson, A and Wood-Charlson, EM and Smith, M and Koch, BJ and Beilsmith, K and Kimbrel, JA and Kellom, M and Hunter, CI and Walls, RL and Schriml, LM and Wilhelm, RC},
title = {MISIP: a data standard for the reuse and reproducibility of any stable isotope probing-derived nucleic acid sequence and experiment.},
journal = {GigaScience},
volume = {13},
number = {},
pages = {},
doi = {10.1093/gigascience/giae071},
pmid = {39399973},
issn = {2047-217X},
support = {IND90024429//USDA/ ; //Purdue University/ ; //Lawrence Berkeley National Laboratory/ ; },
mesh = {*Isotope Labeling/methods ; Reproducibility of Results ; Microbiota/genetics ; Metadata ; Metagenomics/methods ; Sequence Analysis, DNA/methods ; Metagenome ; },
abstract = {DNA/RNA-stable isotope probing (SIP) is a powerful tool to link in situ microbial activity to sequencing data. Every SIP dataset captures distinct information about microbial community metabolism, process rates, and population dynamics, offering valuable insights for a wide range of research questions. Data reuse maximizes the information derived from the labor and resource-intensive SIP approaches. Yet, a review of publicly available SIP sequencing metadata showed that critical information necessary for reproducibility and reuse was often missing. Here, we outline the Minimum Information for any Stable Isotope Probing Sequence (MISIP) according to the Minimum Information for any (x) Sequence (MIxS) framework and include examples of MISIP reporting for common SIP experiments. Our objectives are to expand the capacity of MIxS to accommodate SIP-specific metadata and guide SIP users in metadata collection when planning and reporting an experiment. The MISIP standard requires 5 metadata fields-isotope, isotopolog, isotopolog label, labeling approach, and gradient position-and recommends several fields that represent best practices in acquiring and reporting SIP sequencing data (e.g., gradient density and nucleic acid amount). The standard is intended to be used in concert with other MIxS checklists to comprehensively describe the origin of sequence data, such as for marker genes (MISIP-MIMARKS) or metagenomes (MISIP-MIMS), in combination with metadata required by an environmental extension (e.g., soil). The adoption of the proposed data standard will improve the reuse of any sequence derived from a SIP experiment and, by extension, deepen understanding of in situ biogeochemical processes and microbial ecology.},
}
@article {pmid39399231,
year = {2024},
author = {Scicchitano, D and Foresto, L and Laczny, CC and Cinti, N and Vitagliano, R and Halder, R and Morri, G and Turroni, S and D'Amico, F and Palladino, G and Fiori, J and Wilmes, P and Rampelli, S and Candela, M},
title = {A 15-day pilot biodiversity intervention with horses in a farm system leads to gut microbiome rewilding in 10 urban Italian children.},
journal = {One health (Amsterdam, Netherlands)},
volume = {19},
number = {},
pages = {100902},
pmid = {39399231},
issn = {2352-7714},
abstract = {To provide some glimpses on the possibility of shaping the human gut microbiome (GM) through probiotic exchange with natural ecosystems, here we explored the impact of 15 days of daily interaction with horses on the GM of 10 urban-living Italian children. Specifically, the children were in close contact with the horses in an "educational farm", where they spent almost 10 h/day interacting with the animals. The children's GM was assessed before and after the horse interaction using metabarcoding sequencing and shotgun metagenomics, along with the horses' skin, oral and fecal microbiomes. Targeted metabolomic analysis for GM-produced beneficial metabolites (i.e., short-chain fatty acids) in the children's feces was also performed. Interaction with horses facilitated the acquisition of health-related traits in the children's GM, such as increased diversity, enhanced butyrate production and an increase in several health-promoting species considered to be next-generation probiotics. Among these, the butyrate producers Facecalibacterium prausnitzii and F. duncaniae and a species belonging to the order Christensenellales. Interaction with horses was also associated with increased proportions of Eggerthella lenta, Gordonibacter pamelae and G. urolithinfaciens, GM components known to play a role in the bioconversion of dietary plant polyphenols into beneficial metabolites. Notably, no increase in potentially harmful traits, including toxin genes, was observed. Overall, our pilot study provides some insights on the existence of possible health-promoting exchanges between children and horses microbiomes. It lays the groundwork for an implemented and more systematic enrollment effort to explore the full complexity of human GM rewilding through exchange with natural ecosystems, aligning with the One Health approach.},
}
@article {pmid39398609,
year = {2024},
author = {Lin, S and Chen, Y and Li, H and Chen, T and Lin, Q},
title = {Diagnostic value and clinical use of metagenomic next-generation sequencing for invasive pulmonary aspergillosis.},
journal = {American journal of translational research},
volume = {16},
number = {9},
pages = {4885-4893},
pmid = {39398609},
issn = {1943-8141},
abstract = {OBJECTIVE: To compare the diagnostic efficacy of metagenomic next generation sequencing (mNGS) with traditional fungal culture, (1,3)-β-D glucan (G) test, and galactomannan (GM) test in diagnosing invasive pulmonary aspergillosis (IPA) and to explore the advantages and disadvantages of mNGS for IPA diagnosis.<br><br>METHODS: A retrospective analysis was conducted on 136 patients admitted to the Department of Respiratory and Critical Care Medicine of Affiliated Hospital of Putian University from March 2018 to March 2020. Among them, there were 66 patients with IPA (IPA group) and 70 without (non-IPA group). Baseline data, inflammatory factors, cytokines, and specimens such as bronchoalveolar lavage fluid (BALF) and blood of these patients were collected. Fungal culture test, G test, GM test and mNGS test were performed. Information included for analysis encompassed patients' host factors, clinical features, chest scanning images, laboratory test results, and treatment outcome.<br><br>RESULTS: There was no statistical difference in the baseline data or inflammatory factors in patients between the IPA group and the non-IPA group. Further analysis showed that the sensitivity of mNGS in diagnosing IPA was 53.03%, which was higher than that of traditional fungal culture test (27.27%), G test (31.82%), and GM test (34.85%). Notably, when combining fungal culture, G test, GM test, and mNGS, the sensitivity increased to 69.70%, with a specificity of 97.14%. The sensitivity of the combined test was higher than that any of the tests alone for diagnosing IPA.<br><br>CONCLUSION: mNGS test offers superior diagnostic performance for IPA in comparison to traditional tests, particularly for testing samples like bronchoalveolar lavage fluid and bronchial secretions. The test result remains valuable even after aspergillus treatment. In addition, the use of mNGS in conjunction with other traditional tests, such as fungal culture test, G test, and GM test, can enhance the diagnostic efficacy for IPA.},
}
@article {pmid39398475,
year = {2024},
author = {Kumar, G and Bhadury, P},
title = {Dataset of metagenomic profiles of human gut microbiome from frozen fecal samples sequenced using Illumina and ONT chemistries.},
journal = {Data in brief},
volume = {57},
number = {},
pages = {110961},
pmid = {39398475},
issn = {2352-3409},
abstract = {The data presented in this study are metagenomic profiles of human gut microbiome deduced from frozen fecal samples using two different sequencing chemistries namely, Illumina and Oxford Nanopore Technologies (ONT). The generated data is obtained from genomic DNA extracted from frozen fecal samples collected from a healthy individual on Day 3, Day 5, Day 9, Day 12, and Day 30, in addition to Day 1 (unfrozen). The metagenomic sequence data have been deposited at NCBI SRA as BioProject PRJNA827663. The taxonomic annotation undertaken using MG-RAST showed relative abundance of bacteria represented by different taxonomic levels varied significantly based on two sequencing chemistries. There was distinct temporal variation in the relative abundance of bacteria at different taxonomic levels based on the day of extraction of genomic DNA. This dataset can be used to study differences in functional profiles of human gut microbiome using different sequencing technologies. Moreover, generated data can aid in selection of most appropriate sequencing chemistry to study future human gut microbiome studies based on the appropriate preservation method of fecal samples.},
}
@article {pmid39398427,
year = {2024},
author = {Ji, J and Cai, F and Yuan, C and Huang, C and Zhang, H and Xu, C and Suo, W and Zhu, W and Shi, B and Tang, D and Wang, Y},
title = {Gut Microbiota in Primary Osteoporosis: a Systematic Review.},
journal = {Phenomics (Cham, Switzerland)},
volume = {4},
number = {3},
pages = {293-297},
pmid = {39398427},
issn = {2730-5848},
abstract = {UNLABELLED: The link between gut microbiota (GM) and primary osteoporosis has garnered substantial attention. In this study, we conducted a systematic review encompassing 10 studies that employed high-throughput sequencing methodologies. Notably, the taxonomic profiles exhibited pronounced heterogeneity across reviewed studies. A combined analysis of mechanistical studies screened out potential targets for osteoporosis prevention and treatment. We appraised the limitations in previous studies, and proposed suggestions for optimizing sequencing techniques and experimental designs. Larger-size longitudinal cohorts based on multi-omics and extended phenotypes are recommended to comprehensively characterize the involvement of GM in the pathogenesis of osteoporosis.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s43657-024-00164-y.},
}
@article {pmid39398034,
year = {2024},
author = {Ji, L and Wang, Y and Sun, Y and Ji, L and Wang, X and Liu, Y and Shen, Q and Yang, S and Zhang, W},
title = {Identification and characterization of multiple novel viruses in fecal samples of ruddy shelducks using viral metagenomics methods.},
journal = {Heliyon},
volume = {10},
number = {19},
pages = {e38338},
pmid = {39398034},
issn = {2405-8440},
abstract = {The viral metagenomics approach is an effective technique for investigating and analysing both existing and emerging viruses in humans and diverse animal samples. The ruddy shelduck, a nationally protected secondary key species of wild animals, has become the predominant species among overwintering waterbirds in Qinghai Lake. Viruses carried by ruddy shelducks can potentially infect humans or other animals; however, limited research on the faecal virome of ruddy shelducks is currently available. In the present study, faecal samples of ruddy shelducks collected from Saga County, Shigatse City, Tibet, China, were subjected to viral metagenomic analysis. The predominant viral families identified in ruddy shelduck samples were Picornaviridae, Parvoviridae, Microviridae, Vilyaviridae, Astroviridae, and Caliciviridae. Among these, two picornavirus genomes have been identified as new strains of the genus Megrivirus in the family Parvoviridae. In addition, viruses that infect parasites and bacteria have been identified and characterised. The present study enhances our comprehension of the composition of the viral community in ruddy shelducks faeces and highlights the dynamic nature of viral evolution and the significance of continuous monitoring to assess potential risks to wildlife and public health.},
}
@article {pmid39397942,
year = {2024},
author = {Chen, WY and Lee, CP and Pavlović, J and Pangallo, D and Wu, JH},
title = {Characterization of microbiome, resistome, mobilome, and virulome in anoxic and oxic wastewater treatment processes in Slovakia and Taiwan.},
journal = {Heliyon},
volume = {10},
number = {19},
pages = {e38723},
pmid = {39397942},
issn = {2405-8440},
abstract = {This study presents a comprehensive analysis of samples from urban wastewater treatment plants using anoxic/oxic processes in Slovakia and Taiwan, focusing on microbiome, resistome, mobilome, and virulome, which were analyzed using a shotgun metagenomic approach. Distinct characteristics were observed; in Taiwan, a higher abundance and diversity of antibiotic resistance genes were found in both influent and effluent samples, while there was a higher prevalence of mobile genetic elements and virulence factor genes in Slovakia. Variations were noted in microbial community structures; influent samples in Taiwan were reflected from fecal and hospital sources, and those in Slovakia were derived from environmental elements. At the genus level, the samples from Taiwan's sewage treatment plants were dominated by Cloacibacterium and Bacteroides, while Acinetobacter was predominant in samples from Slovakia. Despite similar antibiotic usage patterns, distinct wastewater characteristics and operational disparities influenced microbiome, resistome, mobilome, and virulome compositions, with limited reduction of most resistance genes by the studied anoxic/oxic processes. These findings underscore the importance of region-specific insights into microbial communities for understanding the dynamics of antimicrobial resistance and pathogenicity in urban wastewater treatment systems. Such insights may lay the groundwork for optimizing treatment processes and reducing the dissemination of antibiotic resistance and pathogenicity genes for safeguarding public health.},
}
@article {pmid39397494,
year = {2024},
author = {Fargeas, M and Faure, F and Douadi, C and Chevarin, C and Birer, A and Sivignon, A and Rodrigues, M and Denizot, J and Billard, E and Barnich, N and Buisson, A},
title = {ChiA: a major player in the virulence of Crohn's disease-associated adherent and invasive Escherichia coli (AIEC).},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2412667},
doi = {10.1080/19490976.2024.2412667},
pmid = {39397494},
issn = {1949-0984},
mesh = {*Crohn Disease/microbiology/pathology ; Humans ; *Escherichia coli/genetics/pathogenicity/metabolism ; Animals ; *Bacterial Adhesion ; Mice ; *Intestinal Mucosa/microbiology/metabolism/pathology ; *Escherichia coli Infections/microbiology ; Virulence ; Disease Models, Animal ; Adhesins, Escherichia coli/metabolism/genetics ; Female ; Male ; Colitis/microbiology/pathology ; Virulence Factors/genetics/metabolism ; Mice, Inbred C57BL ; Mucins/metabolism ; },
abstract = {We investigated the role of ChiA and its associated polymorphisms in the interaction between Crohn's disease (CD)-associated adherent-invasive Escherichia coli (AIEC) and intestinal mucosa. We observed a higher abundance of chiA among the metagenome of CD patients compared to healthy subjects. In dextran sulfate sodium-induced colitis mice model, AIEC-LF82∆chiA colonization was reduced in ileal, colonic and fecal samples compared to wild-type LF82. The binding of ChiA to recombinant human CHI3L1 or mucus was higher with the pathogenic polymorphism. The strength of ChiA-mucin interaction was 300-fold stronger than ChiA-rhCHI3L1. ChiA was able to degrade mucin to promote its growth and enabled LF82 to get closer to epithelial cells. The pathogenic polymorphism of ChiA had a stronger impact on mucus degradation than on the binding capability of AIEC to adhere to the intestinal epithelium. We observed that ChiA could favor an efficient bacterial invasion of intestinal crypts, and that ChiA, especially its pathogenic polymorphism, gives LF82 an advantage to uptake within Peyer's patches, macrophages and mesenteric lymph nodes. All together, these data support the role of ChiA in the virulence of AIEC and show that it could be a promising target to reduce AIEC colonization in patients with CD.},
}
@article {pmid39397304,
year = {2024},
author = {Qing, Z and Jida, Y and Chengxiu, F and Yanli, Y and Xia, L and Sihe, D},
title = {Ralstonia solanacearum Infection Drives the Assembly and Functional Adaptation of Potato Rhizosphere Microbial Communities.},
journal = {The plant pathology journal},
volume = {40},
number = {5},
pages = {498-511},
doi = {10.5423/PPJ.OA.06.2024.0086},
pmid = {39397304},
issn = {1598-2254},
support = {202204BI090024//Yunnan Innovation Guidance and technology-based Enterprise Cultivation Program/ ; },
abstract = {Bacterial wilt caused by Ralstonia solanacearum is a destructive disease that affects potato production, leading to severe yield losses. Currently, little is known about the changes in the assembly and functional adaptation of potato rhizosphere microbial communities during different stages of R. solanacearum infection. In this study, using amplicon and metagenomic sequencing approaches, we analyzed the changes in the composition and functions of bacterial and fungal communities in the potato rhizosphere across four stages of R. solanacearum infection. The results showed that R. solanacearum infection led to significant changes in the composition and functions of bacterial and fungal communities in the potato rhizosphere, with various microbial properties (including α,β-diversity, species composition, and community ecological functions) all being driven by R. solanacearum infection. The relative abundance of some beneficial microorganisms in the potato rhizosphere, including Firmicutes, Bacillus, Pseudomonas, and Mortierella, decreased as the duration of infection increased. Moreover, the related microbial communities played a significant role in basic metabolism and signal transduction; however, the functions involved in soil C, N, and P transformation weakened. This study provides new insights into the dynamic changes in the composition and functions of potato rhizosphere microbial communities at different stages of R. solanacearum infection to adapt to the growth promotion or disease suppression strategies of host plants, which may provide guidance for formulating future strategies to regulate microbial communities for the integrated control of soil-borne plant diseases.},
}
@article {pmid39396970,
year = {2024},
author = {Zu, C and Li, W and Zhang, M and Dong, Y and Fu, S and Feng, J and Hong, R and Huang, H and Hu, Y and Su, J},
title = {Outcome of Pneumocystis Jirovecii pneumonia (PcP) in post-CAR-T patients with hematological malignancies.},
journal = {BMC infectious diseases},
volume = {24},
number = {1},
pages = {1147},
pmid = {39396970},
issn = {1471-2334},
support = {81800178//National Natural Science Foundation of China,China/ ; 81730008//National Natural Science Foundation of China/ ; 82270234//National Natural Science Foundation of China/ ; 2022YFC2304505//National Key Research and Development Program of China/ ; },
mesh = {Humans ; *Pneumonia, Pneumocystis/immunology ; Male ; Female ; Middle Aged ; Retrospective Studies ; *Hematologic Neoplasms/complications ; *Pneumocystis carinii ; Adult ; *Immunocompromised Host ; Immunotherapy, Adoptive/adverse effects ; Aged ; Treatment Outcome ; Opportunistic Infections/microbiology/immunology ; Trimethoprim, Sulfamethoxazole Drug Combination/therapeutic use ; Young Adult ; },
abstract = {BACKGROUND: Pneumocystis jirovecii pneumonia (PcP) is an opportunistic infection associated with immunocompromised patients. The development of novel immunotherapies has promoted the incidence of PcP. This study describes the clinical course and outcome of PcP in chimeric antigen receptor (CAR) T cell recipients with hematological malignancies.<br><br>METHODS: This is a retrospective case series of CAR-T recipients diagnosed with PcP in our center. The cases were all confirmed by metagenomic next-generation sequencing of clinical samples. The demographic, clinical, and outcome data were retrieved from the patients' medical charts and electronic medical record system.<br><br>RESULTS: In total, 8 cases of PcP were identified. The underlying malignancies included T-acute lymphoblastic leukemia (ALL) (n&#x2009;=&#x2009;1), diffuse large B cell lymphoma (DLBCL) (n&#x2009;=&#x2009;4), and B-ALL (n&#x2009;=&#x2009;3). One patient received short-term sulfamethoxazole-trimethoprim (SMZ-TMP) while the others had no prophylaxis. Four patients had neutropenia/lymphopenia at the diagnosis of PcP, and two patients had immunosuppressants within one month before PcP manifestation. The median time from CAR-T infusion to PcP diagnosis was 98.5&#xa0;days (range 52-251). Seven patients recovered from PcP after proper management while one died of septic shock.<br><br>CONCLUSION: PcP can occur after different CAR-T product, and the long-term depletion of immune cells seems to be related to PcP. SMZ-TMP is effective in this setting. More real-world experience of CAR-T therapy is required to assess the incidence and outcome of PcP in this population.},
}
@article {pmid39396943,
year = {2024},
author = {Li, H and Yu, J and Zeng, Z and Liu, C and Zhang, Y and Xia, H and Guo, S},
title = {Clinical and pathological features of cerebrospinal meningitis caused by Pantoea agglomerans : a case report.},
journal = {BMC infectious diseases},
volume = {24},
number = {1},
pages = {1150},
pmid = {39396943},
issn = {1471-2334},
mesh = {Humans ; Female ; *Pantoea/isolation &amp; purification ; Middle Aged ; Meningitis, Bacterial/microbiology/diagnosis/pathology/drug therapy ; Enterobacteriaceae Infections/microbiology/pathology ; Magnetic Resonance Imaging ; Anti-Bacterial Agents/therapeutic use ; },
abstract = {BACKGROUND: Pantoea agglomerans (P. agglomerans) is a gram-negative bacterium that is commonly isolated from plant surfaces, seeds, and the environment. As an opportunistic pathogen, it can cause blood, urinary and soft tissue infections in immunocompromised patients. In central nervous system, P. agglomerans infection has been report in children and immune-compromised patients, however, infection by such bacterium in nontraumatized immune competent adults has not been reported. Here, we report a case of P. agglomerans cerebrospinal meningitis accompanied by positive anti-myeloperoxidase (MPO) antibody in a 49-year-old female who has a history of black fungus planting.<br><br>CASE PRESENTATION: The patient manifested with repeated fever, headache, generalized muscle pain, and neurological defects. Cerebrospinal fluid (CSF) tests revealed a moderately elevated number of polymorphonuclear leukocytes (50-193&#x2009;&#xd7;&#x2009;10[6]/L), low glucose levels (0.54-2.44 mmo1/L), and extremely high protein content (2.42-25.42&#xa0;g/L). Blood tests showed positive anti-myeloperoxidase antibodies lasting for 1.5 year before turning negative. Spine MRI showed thickening and enhancement of the whole spinal meninges. CSF metagenomic next-generation sequencing (mNGS) revealed 75,189 specific DNA reads of P. agglomerans. The patient underwent spinal laminectomy due to meningeal adhesions. Pathological results revealed fibrous tissue proliferation, inflammatory infiltration with focal necrosis and calcification in the dura mater. The patient was successfully treated with sufficient antibiotics at 1-year follow-up.<br><br>CONCLUSIONS: People should be alert to CNS infections caused by P. agglomerans which presented with relatively mild clinical symptoms at onset, especially for those who contucts relevant agricultural and forestry work. The CSF characterization of P. agglomerans meningitis is elevated multiple nuclei white blood cells, significantly reduced glucose content, and markedly increased protein level which may be related to the secondary spinal membrane adhesions.},
}
@article {pmid39396785,
year = {2024},
author = {Su, XS and Zhang, YB and Jin, WJ and Zhang, ZJ and Xie, ZK and Wang, RY and Wang, YJ and Qiu, Y},
title = {Lily viruses regulate the viral community of the Lanzhou lily rhizosphere and indirectly affect rhizosphere carbon and nitrogen cycling.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {176808},
doi = {10.1016/j.scitotenv.2024.176808},
pmid = {39396785},
issn = {1879-1026},
abstract = {The rhizosphere, where plant roots interact intensely with the soil, is a crucial but understudied area in terms of the impact of virus infection. In this study, we investigated the effects of lily symptomless virus (LSV) and cucumber mosaic virus (CMV) on the Lanzhou lily (Lilium davidii var. unicolor) rhizosphere using metagenomics and bioinformatics analysis. We found that virus infection significantly altered soil pH, inorganic carbon, nitrate nitrogen, and total sulfur. Co-infection with LSV and CMV had a greater influence than single infections on the α- and β-diversity of the rhizosphere viral community in which the absolute abundance of certain virus families (Siphoviridae, Podoviridae, and Myoviridae) increased significantly, whereas bacteria, fungi, and archaea remained relatively unaffected. These altered virus populations influenced the rhizosphere microbial carbon and nitrogen cycles by exerting top-down control on bacteria. Co-infection potentially weakened rhizosphere carbon fixation and promoted processes such as methane oxidation, nitrification, and denitrification. In addition, the co-occurrence network of bacteria and viruses in the rhizosphere revealed substantial changes in microbial community composition under co-infection. Our partial-least-squares path model confirmed that the diversity of the rhizosphere viral community indirectly regulated the carbon and nitrogen cycling functions of the microbial community, thus affecting the accumulation of carbon and nitrogen nutrients in the soil. Our results are the first report of the effects of virus infection on the lily rhizosphere, particularly for co-infection; they therefore complement research on the plant virus pathogenic mechanisms, and increase our understanding of the ecological role of rhizosphere soil viruses.},
}
@article {pmid39396767,
year = {2024},
author = {Zhao, F and Tie, N and Kwok, LY and Ma, T and Wang, J and Man, D and Yuan, X and Li, H and Pang, L and Shi, H and Ren, S and Yu, Z and Shen, X and Li, H and Zhang, H},
title = {Baseline gut microbiome as a predictive biomarker of response to probiotic adjuvant treatment in gout management.},
journal = {Pharmacological research},
volume = {},
number = {},
pages = {107445},
doi = {10.1016/j.phrs.2024.107445},
pmid = {39396767},
issn = {1096-1186},
abstract = {Gout is characterized by dysregulation of uric acid (UA) metabolism, and the gut microbiota may serve as a regulatory target. This two-month randomized, double-blind, placebo-controlled trial aimed to investigate the additional benefits of coadministering Probio-X alongside febuxostat. A total of 160 patients with gout were randomly assigned to either the probiotic group (n = 120; Probio-X [1 ×10[11] CFU/day] with febuxostat) or the placebo group (n = 40; placebo material with febuxostat). Coadministration of Probio-X significantly decreased serum UA levels and the rate of acute gout attacks (P < 0.05). Based on achieving a target sUA level (360 μmol/L) after the intervention, the probiotic group was further subdivided into probiotic-responsive (ProA; n = 54) and probiotic-unresponsive (ProB; n = 66) subgroups. Post-intervention clinical indicators, metagenomic, and metabolomic changes in the ProB and placebo groups were similar, but differed from those in the ProA group, which exhibited significantly lower levels of acute gout attack, gout impact score, serum indicators (UA, XOD, hypoxanthine, and IL-1β), and fecal gene abundances of UA-producing pathways (KEGG orthologs of K13479 and K01487; gut metabolic modules for formate conversion and lactose and galactose degradation). Additionally, the ProA group showed significantly higher levels (P < 0.05) of gut SCFAs-producing bacteria and UA-related metabolites (xanthine, hypoxanthine, bile acids) after the intervention. Finally, we established a gout metagenomic classifier to predict probiotic responsiveness based on subjects' baseline gut microbiota composition. Our results indicate that probiotic-driven therapeutic responses are highly individual, with the probiotic-responsive cohort benefitting significantly from probiotic coadministration. This trial was registered in the Chinese Clinical Trial Registry with the identifier number ChiCTR1900028232.},
}
@article {pmid39395606,
year = {2024},
author = {Wang, E and Sun, H and Xing, F and Zheng, Y and Chen, P and Lyu, T and Liu, R and Li, X and Dong, R and Guo, J},
title = {Metagenomic analysis reveals metabolic mechanism of enhancing lignocellulosic anaerobic digestion mediated by CO2/O2-nanobubble water.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {131622},
doi = {10.1016/j.biortech.2024.131622},
pmid = {39395606},
issn = {1873-2976},
abstract = {Nanobubble water (NW) has been reported to enhance anaerobic digestion (AD), but its influence on the metabolic pathways of microorganisms remains unclear. In this study, the specific methane yields of rice straw in the CO2NW and O2NW treatments increased by 6.9% and 18.3%, respectively. The electron transport system (ETS) and coenzyme F420 activities were enhanced by the addition of NW. Metagenomic analysis showed that the abundances of most enzymes in the acidification were significantly increased by both CO2NW and O2NW. Regarding methanogenesis, CO2NW promoted the expression of genes encoding enzymes of hydrogenotrophic methanogenesis, while O2NW stimulated both the acetoclastic and hydrogenotrophic methanogenesis. With the addition of O2NW, the expressions of modules related to the tricarboxylic acid (TCA) cycle and oxidative phosphorylation were enhanced, resulting in increased ATP production. This study provided fundamental evidence of the metabolic pathways of microorganisms mediated by NW at each stage of AD.},
}
@article {pmid39388213,
year = {2024},
author = {Lu, R and Dumonceaux, T and Anzar, M and Zovoilis, A and Antonation, K and Barker, D and Corbett, C and Nadon, C and Robertson, J and Eagle, SHC and Lung, O and Rudar, J and Surujballi, O and Laing, C},
title = {MNBC: A multithreaded minimizer-based naïve bayes classifier for improved metagenomic sequence classification.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btae601},
pmid = {39388213},
issn = {1367-4811},
abstract = {MOTIVATION: State-of-the-art tools for classifying metagenomic sequencing reads provide both rapid and accurate options, although the combination of both in a single tool is a constantly improving area of research. The machine learning-based Naïve Bayes Classifier (NBC) approach provides a theoretical basis for accurate classification of all reads in a sample.<br><br>RESULTS: We developed the multithreaded Minimizer-based Na&#xef;ve Bayes Classifier (MNBC) tool to improve the NBC approach by applying minimizers, as well as plurality voting for closely-related classification scores. A standard reference- and test-sequence framework using simulated variable-length reads benchmarked MNBC with six other state-of-the-art tools: MetaMaps, Ganon, Kraken2, KrakenUniq, CLARK and Centrifuge. We also applied MNBC to the "marine" and "strain-madness" short-read metagenomic datasets in the Critical Assessment of Metagenome Interpretation (CAMI) II challenge using a corresponding database from the time. MNBC efficiently identified reads from unknown microorganisms, and exhibited the highest species- and genus-level precision and recall on short reads, as well as the highest species-level precision on long reads. It also achieved the highest accuracy on the "strain-madness" dataset.<br><br>AVAILABILITY: MNBC is freely available at: Https://github.com/ComputationalPathogens/MNBC.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}
@article {pmid39387577,
year = {2024},
author = {Beck, KL and Haiminen, N and Agarwal, A and Carrieri, AP and Madgwick, M and Kelly, J and Pylro, V and Kawas, B and Wiedmann, M and Ganda, E},
title = {Development and evaluation of statistical and artificial intelligence approaches with microbial shotgun metagenomics data as an untargeted screening tool for use in food production.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0084024},
doi = {10.1128/msystems.00840-24},
pmid = {39387577},
issn = {2379-5077},
abstract = {UNLABELLED: The increasing knowledge of microbial ecology in food products relating to quality and safety and the established usefulness of machine learning algorithms for anomaly detection in multiple scenarios suggests that the application of microbiome data in food production systems for anomaly detection could be a valuable approach to be used in food systems. These methods could be used to identify ingredients that deviate from their typical microbial composition, which could indicate food fraud or safety issues. The objective of this study was to assess the feasibility of using shotgun sequencing data as input into anomaly detection algorithms using fluid milk as a model system. Contrastive principal component analysis (PCA), cluster-based methods, and explainable artificial intelligence (AI) were evaluated for the detection of two anomalous sample classes using longitudinal metagenomic profiling of fluid milk compared to baseline (BL) samples collected under comparable circumstances. Traditional methods (alpha and beta diversity, clustering-based contrastive PCA, multidimensional scaling, and dendrograms) failed to differentiate anomalous sample classes; however, explainable AI was able to classify anomalous vs baseline samples and indicate microbial drivers in association with antibiotic use. We validated the potential for explainable AI to classify different milk sources using larger publicly available fluid milk 16S rDNA sequencing data sets and demonstrated that explainable AI is able to differentiate between milk storage methods, processing stages, and seasons. Our results indicate that the application of artificial intelligence continues to hold promise in the realm of microbiome data analysis and could present further opportunities for downstream analytic automation to aid in food safety and quality.<br><br>IMPORTANCE: We evaluated the feasibility of using untargeted metagenomic sequencing of raw milk for detecting anomalous food ingredient content with artificial intelligence methods in a study specifically designed to test this hypothesis. We also show through analysis of publicly available fluid milk microbial data that our artificial intelligence approach is able to successfully predict milk in different stages of processing. The approach could potentially be applied in the food industry for safety and quality control.},
}
@article {pmid39387572,
year = {2024},
author = {Ueno, K and Sawada, S and Ishibashi, M and Kanda, Y and Shimizu, H and Toya, Y},
title = {Identification of a novel NADPH generation reaction in the pentose phosphate pathway in Escherichia coli using mBFP.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0027624},
doi = {10.1128/jb.00276-24},
pmid = {39387572},
issn = {1098-5530},
abstract = {NADPH is a redox cofactor that drives the anabolic reactions. Although major NADPH generation reactions have been identified in Escherichia coli, some minor reactions have not been identified. In the present study, we explored novel NADPH generation reactions by monitoring the fluorescence dynamics after the addition of carbon sources to starved cells, using a metagenome-derived blue fluorescent protein (mBFP) as an intracellular NADPH reporter. Perturbation analyses were performed on a glucose-6-phosphate isomerase (PGI) deletion strain and its parental strain. Interestingly, mBFP fluorescence increased not only in the parental strain but also in the ΔPGI strain after the addition of xylose. Because the ΔPGI strain cannot metabolize xylose through the oxidative pentose phosphate pathway, this suggests that an unexpected NADPH generation reaction contributes to an increase in fluorescence. To unravel this mystery, we deleted the NADPH generation enzymes including transhydrogenase, isocitrate dehydrogenase, NADP[+]-dependent malic enzyme, glucose-6-phosphate dehydrogenase (G6PDH), and 6-phosphogluconate dehydrogenase (6PGDH) in the ΔPGI strain, and revealed that G6PDH and 6PGDH contribute to an increase in fluorescence under xylose conditions. In vitro assays using purified enzymes showed that G6PDH can produce NADPH using erythrose-4-phosphate (E4P) as a substitute for glucose-6-phosphate. Because the Km (0.65 mM) for E4P was much higher than the reported intracellular E4P concentrations in E. coli, little E4P must be metabolized through this bypass in the parental strain. However, the flux would increase when E4P accumulates in the cells owing to genetic modifications. This finding provides a metabolic engineering strategy for generating NADPH to produce useful compounds using xylose as a carbon source.IMPORTANCEBecause NADPH is consumed during the synthesis of various useful compounds, enhancing NADPH regeneration is highly desirable in metabolic engineering. In this study, we explored novel NADPH generation reactions in Escherichia coli using a fluorescent NADPH reporter and found that glucose-6-phosphate dehydrogenase can produce NADPH using erythrose-4-phosphate as a substrate under xylose conditions. Xylose is an abundant sugar in nature and is an attractive carbon source for bioproduction. Therefore, this finding contributes to novel pathway engineering strategies using a xylose carbon source in E. coli to produce useful compounds that consume NADPH for their synthesis.},
}
@article {pmid39395603,
year = {2024},
author = {Wang, P and Lu, B and Chai, X},
title = {Novel insights into self-defense function of anammox sludge under magnesium ions (Mg[2+]) stress based on Mg[2+] transport system.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {131615},
doi = {10.1016/j.biortech.2024.131615},
pmid = {39395603},
issn = {1873-2976},
abstract = {Magnesium ion (Mg[2+]) plays an important role in the accumulation and stability of anaerobic ammonium-oxidizing bacteria (AnAOB). In this study, the response of anammox sludge to Mg[2+] was comprehensively investigated by performance evaluation and metagenomics analysis. Appropriate Mg[2+] (0.8 mmol/L) could improve the nitrogen removal performance, AnAOB activity, and the synthesis potential of some hydrophobic substances, while high Mg[2+] (>1.6 mmol/L) has a negative effect. Meanwhile, Mg[2+] transmembrane transport theory was introduced to reveal the response principle of AnAOB to Mg[2+] from a novel insight. AnAOB may have a self-defense function based on the PhoQ/PhoP-MgtAB system. Low extracellular Mg[2+] will activate this function to enhance Mg[2+] influx, thereby improving the intracellular metabolism of AnAOB. Excessive Mg[2+], however, dormant this function and induces Mg[2+] efflux, which may decrease the intracellular Mg[2+] and thus affect AnAOB metabolism. These findings provide valuable references for the Mg[2+] regulation of anammox-based process.},
}
@article {pmid39395415,
year = {2024},
author = {de Flamingh, A and Gnoske, TP and Kerbis Peterhans, JC and Simeonovski, VA and Gitahi, N and Mwebi, O and Agwanda, BR and Catchen, JM and Roca, AL and Malhi, RS},
title = {Compacted hair in broken teeth reveals dietary prey of historic lions.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2024.09.029},
pmid = {39395415},
issn = {1879-0445},
abstract = {With recent advances, nuclear genome data for phylogenomic analyses can now be sequenced from minuscule quantities of DNA[1] and from specimens that are more than a million years old.[2] DNA analysis from hair is a well-established approach[3] widely used in forensic science[4] and wildlife conservation.[5] Hair samples can be effectively decontaminated[6] and can be used to identify the mammalian species from which the hair was shed.[7][,][8] We aimed to use advances optimized for degraded DNA to systematically identify dietary prey species from hair compacted in the teeth of two Tsavo lions that lived during the 1890s in Kenya (see description of samples in the STAR Methods and Patterson[9] and Kerbis Peterhans and Gnoske[10] for background on the Tsavo "man-eaters"). Analysis of hair DNA identified giraffe, human, oryx, waterbuck, wildebeest, and zebra as prey and also identified hair that originated from lion. DNA preservation allowed for analyses of complete mitogenome profiles of zebra, giraffe, and lion. Giraffe mitogenomes are phylogeographically partitioned, and we found that the lions ate at least two individuals that belong to a subspecies of Masai giraffe (Giraffa tippelskirchi tippelskirchi) typically found in southeast Kenya. The lion mitogenome from a hair sample was identical to the Tsavo lion endogenous mitogenome and most closely matched other East African lions from Kenya and Tanzania. Our approach enables a better understanding of the hunting behaviors, diets, and ecology of historical individuals, populations, and species and holds promise for extinct populations and species.},
}
@article {pmid39395412,
year = {2024},
author = {Talwar, C and Davuluri, GVN and Kamal, AHM and Coarfa, C and Han, SJ and Veeraragavan, S and Parsawar, K and Putluri, N and Hoffman, K and Jimenez, P and Biest, S and Kommagani, R},
title = {Identification of distinct stool metabolites in women with endometriosis for non-invasive diagnosis and potential for microbiota-based therapies.},
journal = {Med (New York, N.Y.)},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.medj.2024.09.006},
pmid = {39395412},
issn = {2666-6340},
abstract = {BACKGROUND: Endometriosis, a poorly studied gynecological condition, is characterized by the presence of ectopic endometrial lesions resulting in pelvic pain, inflammation, and infertility. These associated symptoms contribute to a significant burden, often exacerbated by delayed diagnosis. Current diagnostic methods involve invasive procedures, and existing treatments provide no cure.<br><br>METHODS: Microbiome-metabolome signatures in stool samples from individuals with and without endometriosis were determined using unbiased metabolomics and 16S bacteria sequencing. Functional studies for selected microbiota-derived metabolites were conducted in&#xa0;vitro using patient-derived cells and in&#xa0;vivo by employing murine and human xenograft pre-clinical disease models.<br><br>FINDINGS: We discovered a unique bacteria-derived metabolite signature intricately linked to endometriosis. The altered fecal metabolite profile exhibits a strong correlation with that observed in inflammatory bowel disease (IBD), revealing intriguing connections between these two conditions. Notably, we validated 4-hydroxyindole, a gut-bacteria-derived metabolite that is lower in stool samples of endometriosis. Extensive in&#xa0;vivo studies found that 4-hydroxyindole suppressed the initiation and progression of endometriosis-associated inflammation and hyperalgesia in heterologous mouse and in pre-clinical models of the disease.<br><br>CONCLUSIONS: Our findings are the first to provide a distinct stool metabolite signature in women with endometriosis, which could serve as stool-based non-invasive diagnostics. Further, the gut-microbiota-derived 4-hydroxyindole poses as a therapeutic candidate for ameliorating endometriosis.<br><br>FUNDING: This work was funded by the NIH/NICHD grants (R01HD102680, R01HD104813) and a Research Scholar Grant from the American Cancer Society to R.K.},
}
@article {pmid39395391,
year = {2024},
author = {Gong, K and Peng, C and Hu, S and Xie, W and Chen, A and Liu, T and Zhang, W},
title = {Aging of biodegradable microplastics and their effect on soil properties: Control from soil water.},
journal = {Journal of hazardous materials},
volume = {480},
number = {},
pages = {136053},
doi = {10.1016/j.jhazmat.2024.136053},
pmid = {39395391},
issn = {1873-3336},
abstract = {The ecological risks of biodegradable microplastics (BMPs) to soil ecosystems have received increasing attention. This study investigates the impacts of polylactic acid microplastics (PLA-MPs) and polybutylene adipate terephthalate microplastics (PBAT-MPs) on soil properties of black soil (BS) and fluvo-aquic soil (FS) under three water conditions including dry (Dry), flooded (FL), and alternate wetting and drying (AWD). The results show that BMPs exhibited more evident aging under Dry and AWD conditions compared to FL condition. However, BMPs aging under FL condition induced more substantial changes in soil properties, especially dissolved organic carbon (DOC) concentrations, than under Dry and AWD conditions. BMPs also increased the humification degree of soil dissolved organic matter (DOM), particularly in BS. Metagenomic analysis of PBAT-MPs treatments showed different changes in microbial community structure depending on soil moisture. Under Dry conditions, PBAT-MPs enhance the ammonium-producing process of soil microbial communities. Genes related to N nitrification and benzene degradation were enriched under AWD conditions. In contrast, PBAT-MPs do not change the abundance of genes related to the N cycle under FL conditions but significantly reduce genes related to benzene degradation. This reduction in benzene degradation genes under FL condition might potentially slow down the degradation of PBAT-MPs, and could lead to temporary accumulation of benzene-related intermediates. These findings highlight the complex interactions between BMPs, soil properties, and microbial communities, emphasizing the need for comprehensive evaluations of BMPs' environmental impacts under varying soil water conditions.},
}
@article {pmid39395082,
year = {2024},
author = {de Farias, BO and Saggioro, EM and Montenegro, KS and Magaldi, M and Santos, HSO and Gonçalves-Brito, AS and Pimenta, RL and Ferreira, RG and Spisso, BF and Pereira, MU and Bianco, K and Clementino, MM},
title = {Metagenomic insights into plasmid-mediated antimicrobial resistance in poultry slaughterhouse wastewater: antibiotics occurrence and genetic markers.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {39395082},
issn = {1614-7499},
support = {E-21/201.271/2021//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; E-26/210.882/2021//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; 304571/2021-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; },
abstract = {Slaughterhouse wastewater represents important convergence and concentration points for antimicrobial residues, bacteria, and antibiotic resistance genes (ARG), which can promote antimicrobial resistance propagation in different environmental compartments. This study reports the assessment of the metaplasmidome-associated resistome in poultry slaughterhouse wastewater treated by biological processes, employing metagenomic sequencing. Antimicrobial residues from a wastewater treatment plant (WWTP) that treats poultry slaughterhouse influents and effluents were investigated through high-performance liquid chromatography coupled to tandem mass spectrometry (HPLC-MS/MS). Residues from the macrolide, sulfonamide, and fluoroquinolone classes were detected, the latter two persisting after the wastewater treatment. The genetic markers 16S rRNA rrs (bacterial community) and uidA (Escherichia coli) were investigated by RT-qPCR and the sul1 and int1 genes by qPCR. After treatment, the 16S rRNA rrs, uidA, sul1, and int1 markers exhibited reductions of 0.67, 1.07, 1.28, and 0.79 genes copies, respectively, with no statistical significance (p > 0.05). The plasmidome-focused metagenomics sequences (MiSeq platform (Illumina®)) revealed more than 100 ARG in the WWTP influent, which can potentially confer resistance to 14 pharmacological classes relevant in the human and veterinary clinical contexts, in which the qnr gene (resistance to fluoroquinolones) was the most prevalent. Only 7.8% of ARG were reduced after wastewater treatment, and the remaining 92.2% were associated with an increase in the prevalence of ARG linked to multidrug efflux pumps, substrate-specific for certain classes of antibiotics, or broad resistance to multiple medications. These data demonstrate that wastewater from poultry slaughterhouses plays a crucial role as an ARG reservoir and in the spread of AMR into the environment.},
}
@article {pmid39394961,
year = {2024},
author = {Branck, T and Hu, Z and Nickols, WA and Walsh, AM and Bhosle, A and Short, MI and Nearing, JT and Asnicar, F and McIver, LJ and Maharjan, S and Rahnavard, A and Louyakis, A and Badri, DV and Brockel, C and Thompson, KN and Huttenhower, C},
title = {Comprehensive profile of the companion animal gut microbiome integrating reference-based and reference-free methods.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae201},
pmid = {39394961},
issn = {1751-7370},
abstract = {The gut microbiome of companion animals is relatively underexplored, despite its relevance to animal health, pet owner health, and basic microbial community biology. Here, we provide the most comprehensive analysis of the canine and feline gut microbiomes to date, incorporating 2639 stool shotgun metagenomes (2272 dog and 367 cat) spanning 14 publicly available datasets (n = 730) and 8 new study populations (n = 1909). These are compared with 238 and 112 baseline human gut metagenomes from the Human Microbiome Project 1-II and a traditionally living Malagasy cohort, respectively, processed in a manner identical to the animal metagenomes. All microbiomes were characterized using reference-based taxonomic and functional profiling, as well as de novo assembly yielding metagenomic assembled genomes clustered into species-level genome bins. Companion animals shared 184 species-level genome bins not found in humans, whereas 198 were found in all three hosts. We applied novel methodology to distinguish strains of these shared organisms either transferred or unique to host species, with phylogenetic patterns suggesting host-specific adaptation of microbial lineages. This corresponded with functional divergence of these lineages by host (e.g., differences in metabolic and antibiotic resistance genes) likely important to companion animal health. This study provides the largest resource to date of companion animal gut metagenomes and greatly contributes to our understanding of the "One Health" concept of a shared microbial environment among humans and companion animals, affecting infectious diseases, immune response, and specific genetic elements.},
}
@article {pmid39394504,
year = {2024},
author = {Passarini, MRZ and Robayo, MIG and Ottoni, JR and Duarte, AWF and Rosa, LH},
title = {Biotechnological potential in agriculture of soil Antarctic microorganisms revealed by omics approach.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {40},
number = {11},
pages = {345},
pmid = {39394504},
issn = {1573-0972},
support = {N&#xba; 205/2021//Program Institutional Triple Agenda EDITAL PRPPG/ ; },
mesh = {*Soil Microbiology ; Antarctic Regions ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; *Agriculture ; *Fungi/classification/genetics/isolation &amp; purification/metabolism ; *Biotechnology ; *Metagenomics ; High-Throughput Nucleotide Sequencing ; Soil/chemistry ; Phylogeny ; Nitrogen/metabolism ; Microbiota ; },
abstract = {The biotechnological potential for agricultural applications in the soil in the thawing process on Whalers Bay, Deception Island, Antarctica was evaluated using a metagenomic approach through high-throughput sequencing. Approximately 22.70% of the sequences were affiliated to the phyla of the Bacteria dominion, followed by 0.26% to the Eukarya. Proteobacteria (Bacteria) and Ascomycota (Fungi) were the most abundant phyla. Thirty-two and thirty-six bacterial and fungal genera associated with agricultural biotechnological applications were observed. Streptomyces and Pythium were the most abundant genera related to the Bacteria and Oomycota, respectively. The main agricultural application associated with bacteria was nitrogen affixation; in contrast for fungi, was associated with phytopathogenic capabilities. The present study showed the need to use metagenomic technology to understand the dynamics and possible metabolic pathways associated with the microbial communities present in the soil sample in the process of thawing recovered from the Antarctic continent, which presented potential application in processes of agro-industrial interest.},
}
@article {pmid39394213,
year = {2024},
author = {Neshat, SA and Santillan, E and Seshan, H and Wuertz, S},
title = {Author Correction: Non-redundant metagenome-assembled genomes of activated sludge reactors at different disturbances and scales.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {1120},
doi = {10.1038/s41597-024-03957-y},
pmid = {39394213},
issn = {2052-4463},
}
@article {pmid39393653,
year = {2024},
author = {Li, Y and Huang, F and Dong, S and Liu, L and Lin, L and Li, Z and Zheng, Y and Hu, Z},
title = {Microbiota succession, species interactions, and metabolic functions during autotrophic biofloc formation in zero-water-exchange shrimp farming without organic carbon supplements.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {131584},
doi = {10.1016/j.biortech.2024.131584},
pmid = {39393653},
issn = {1873-2976},
abstract = {Autotrophic bioflocs (ABF) exhibits lower energy consumption, more environment-friendly and cost-effective than heterotrophic bioflocs depending on organic carbon supplements. Whereas ABF has not been widely applied to aquaculture production. Here, ABF successfully performed to control ammonia and nitrite under harmless levels even when carbon-to-nitrogen ratio reduced to 2.0, during 12-week shrimp farming in commercial scale. ABF was mainly dominated by bacteria of Proteobacteria, Bacteroidota, Chloroflexi and eukaryotes of Bacillariophyta, Rotifera, Ciliophora. A notable shift occurred in ABF with the significant decreases of Proteobacteria and Rotifera replaced by Bacteroidota, Chloroflexi, and Bacillariophyta after four weeks. Nitrogen metabolism was synergistically executed by bacteria and microalgae, especially the positive interaction between Nitrospira and Halamphora for ABF nitrification establishment. Metagenomics confirmed the complete functional genes of key bacteria related to the cycling of carbon, nitrogen, and phosphorus by ABF. This study may promote the development application of ABF in low-carbon shrimp aquaculture.},
}
@article {pmid39393455,
year = {2024},
author = {Wang, R and Lu, P and Chen, F and Huang, Y and Ding, H and Cheng, T},
title = {Groundwater Resistant Gene Accumulation in Mining-Agriculture Complex Zones: Insights from Metagenomic Analysis of Subterranean Mineral and Terrestrial Agricultural Interactions.},
journal = {Environmental research},
volume = {},
number = {},
pages = {120138},
doi = {10.1016/j.envres.2024.120138},
pmid = {39393455},
issn = {1096-0953},
abstract = {During the Mining-Agriculture Complex Areas, the mining and agriculture activities could lead to an excessive presence of sulfate content in the regional groundwater. Sulfate exhibits the potential to influence the positive accumulation of RGs, although its mechanisms remain inadequately explored. To address this gap, this study analyzed the RGs buildup mechanisms in the groundwater of the mining-agriculture complex area. Results showed a widespread presence of antibiotic resistance genes (ARGs) and metal resistance genes (MRGs), especially in coal-seams crevice groundwater. And iron and sulfur are primary environmental factors conducive to RGs accumulation through a synergistic interaction. Microbial annotation of gene sets sourced from coal-seams crevice groundwater samples unveiled part of sulfur-metabolizing microorganisms that were hosts of both ARGs and MRGs. Mechanistic insights revealed that iron may stimulates reactive oxygen species (ROS) generation, facilitating RGs accumulation, while adjusting sulfur metabolism and the synthesis of iron-sulfur clusters, thereby augmenting microbial growth which as predominant hosts of RGs, thereby intensifying the buildup of RGs.},
}
@article {pmid39393325,
year = {2024},
author = {Yang, C and Huang, B and Lin, J and Yang, Q and Guo, Y and Liu, D and Sun, B},
title = {Isolation and screening of high biofilm producing lactic acid bacteria, and exploration of its effects on the microbial hazard in corn straw silage.},
journal = {Journal of hazardous materials},
volume = {480},
number = {},
pages = {136009},
doi = {10.1016/j.jhazmat.2024.136009},
pmid = {39393325},
issn = {1873-3336},
abstract = {Silage is a well-established method for preserving feed. However, the preparation process still poses several potential microbial hazards. Lactic acid bacteria exhibiting a biofilm phenotype are considered the most advanced 'fourth-generation probiotics' due to their significant potential in enhancing fermentation quality. In this study, a strain of high-biofilm-producing lactic acid bacteria (HBP-LAB) was successfully isolated from silage samples using the crystal violet method and designated as Lactiplantibacillus plantarum S23Y. This strain was subsequently used as an inoculant in corn straw for experimental purposes. The results indicated that it effectively reduced dry matter loss caused by microorganisms, thereby enhancing the retention of dry matter in silage. Following aerobic exposure, this strain was able to maintain the population of Lactobacillus and the concentration of lactic acid, which significantly decreased the likelihood of yeast-induced aerobic spoilage and improved the aerobic stability of the silage. However, it is important to note that this HBP-LAB did not have a significant impact on antibiotic resistance genes (ARGs) or mobile genetic elements (MGEs) in the silage. In conclusion, using S23Y as a representative strain, we have demonstrated that HBP-LAB can enhance the fermentation quality of silage to a certain extent and mitigate the detrimental effects of microorganisms. The findings of this study provide valuable insights for the application of lactic acid bacteria with a biofilm phenotype in silage fermentation.},
}
@article {pmid39393228,
year = {2024},
author = {Dey, G and Maity, JP and Banerjee, P and Sharma, RK and Das, K and Gnanachandrasamy, G and Wang, CW and Lin, PY and Wang, SL and Chen, CY},
title = {Evaluation and mitigation of potentially toxic elements contamination in mangrove ecosystem: Insights into phytoremediation and microbial perspective.},
journal = {Marine pollution bulletin},
volume = {209},
number = {Pt A},
pages = {117035},
doi = {10.1016/j.marpolbul.2024.117035},
pmid = {39393228},
issn = {1879-3363},
abstract = {Mangroves, essential coastal ecosystems, are threatened by human-induced Potentially-toxic-elements (PTEs) pollution. This study analyzed PTEs distribution, phytoremediation potential, and rhizosphere microbial communities in Taiwan's Xinfeng mangrove forest. Significant variations in physicochemical and PTEs concentrations were observed across adjacent water bodies, with moderate contamination in the river, estuary, and overlying water of mangroves sediment. The partition-coefficient showed the mobility of Bi, Pb, Co, and Sr at the water-sediment interface. The geochemical-indices revealed high Bi and Pb contamination and moderate Zn, Sr, Cu, and Cd contamination in sediment. The overall pollution indices indicated the significant contamination, while moderate ecological risk was found for Cd (40 ≤ Er[i] < 80). Mangroves Kandelia obovata and Avicennia marina exhibited promising PTEs phytoremediation potential (Bi, Cd, Mn, Sr, and Co). Metagenomics indicated a diverse microbial community with N-fixation, P-solubilization, IAA synthesis, and PTEs-resistance genes. These findings underscore the need for targeted conservation to protect these critical habitats.},
}
@article {pmid39392286,
year = {2024},
author = {Rey Redondo, E and Leung, SKK and Yung, CCM},
title = {Genomic and biogeographic characterisation of the novel prasinovirus Mantoniella tinhauana virus 1.},
journal = {Environmental microbiology reports},
volume = {16},
number = {5},
pages = {e70020},
pmid = {39392286},
issn = {1758-2229},
support = {26100521//Research Grants Council, University Grants Committee, Hong Kong/ ; },
mesh = {*Genome, Viral/genetics ; *Phylogeny ; Host Specificity ; Seawater/virology ; China ; Genomics ; Phycodnaviridae/genetics/isolation &amp; purification/classification ; Phylogeography ; Chlorophyta/virology/genetics ; },
abstract = {Mamiellophyceae are a ubiquitous class of unicellular green algae in the global ocean. Their ecological importance is highlighted in studies focused on the prominent genera Micromonas, Ostreococcus, and Bathycoccus. Mamiellophyceae are susceptible to prasinoviruses, double-stranded DNA viruses belonging to the nucleocytoplasmic large DNA virus group. Our study represents the first isolation of a prasinovirus in the South China Sea and the only one to infect the globally distributed genus Mantoniella. We conducted a comparative analysis with previously identified viral relatives, encompassing morphological characteristics, host specificity, marker-based phylogenetic placement, and whole-genome sequence comparisons. Although it shares morphological and genetic similarities with established prasinoviruses, this novel virus showed distinct genetic traits, confining its infection to the species Mantoniella tinhauana. We also explored the global biogeography of this prasinovirus and its host by mapping metagenomic data and analysing their relationship with various environmental parameters. Our results demonstrate a pronounced link between the virus and its host, both found predominantly in higher latitudes in the surface ocean. By gaining an increased understanding of the relationships between viruses, hosts, and environments, researchers can better make predictions and potentially implement measures to mitigate the consequences of climate change on oceanic processes.},
}
@article {pmid39390720,
year = {2024},
author = {Dzhuraeva, M and Bobodzhanova, K and Birkeland, NK},
title = {The metagenomic landscape of a high-altitude geothermal spring in Tajikistan reveals a novel Desulfurococcaceae member, Zestomicrobium tamdykulense gen. nov., sp. nov.},
journal = {MicrobiologyOpen},
volume = {13},
number = {5},
pages = {e70004},
doi = {10.1002/mbo3.70004},
pmid = {39390720},
issn = {2045-8827},
support = {CPEA-LT-2017/10061//Norwegian Directorate for Higher Education and Skills (HK-dir)/ ; },
mesh = {*Hot Springs/microbiology ; *Phylogeny ; Tajikistan ; *Altitude ; Metagenomics ; Archaea/genetics/classification ; Metagenome ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Bacteria/genetics/classification/isolation &amp; purification ; },
abstract = {Metagenomic analysis was conducted to assess the microbial community in the high-altitude Tamdykul geothermal spring in Tajikistan. This analysis yielded six high-quality bins from the members of Thermaceae, Aquificaceae, and Halothiobacillaceae, with a 41.2%, 19.7%, and 18.1% share in the total metagenome, respectively. Minor components included Schleiferia thermophila (1.6%) and members of the archaeal taxa Pyrobaculum (1.2%) and Desulfurococcaceae (0.7%). Further analysis of the metagenome-assembled genome (MAG) from the Desulfurococcaceae family (MAG002) revealed novel taxonomy with only 80.95% closest placement average nucleotide identity value to its most closely related member of the Desulfurococcaceae family, which is part of the Thermoproteota phylum comprising hyperthermophilic members widespread in geothermal environments. MAG002 consisted of 1.3 Mbp, distributed into 48 contigs with 1504 predicted coding sequences, had an average GC content of 41.3%, a completeness and contamination rate of 98.7% and 2.6%, respectively, and branched phylogenetically between the Ignisphaera and Zestosphaera lineages. Digital DNA-DNA hybridization values compared with Ignisphaera aggregans and Zestosphaera tikiterensis were 33.7% and 19.4%, respectively, suggesting that this MAG represented a novel species and genus. Its 16S rRNA gene contained a large 421 bp intron. It encodes a complete gluconeogenesis pathway involving a bifunctional fructose-1,6-bisphosphate phosphatase/aldolase; however, the glycolysis pathway is incomplete. The ribulose monophosphate pathway enzymes could be used for pentose synthesis. MAG002 encodes several hydrogen-evolving hydrogenases, with possible roles as hydrogen sinks during fermentation. We propose the name Zestomicrobium tamdykulense gen. nov. sp. nov. for this organism; it is the first thermophilic genome reported from Tajikistan.},
}
@article {pmid39390034,
year = {2024},
author = {Delanghe, L and De Boeck, I and Van Malderen, J and Allonsius, CN and Van Rillaer, T and Bron, PA and Claes, I and Hagendorens, M and Lebeer, S and Leysen, J},
title = {Mild atopic dermatitis is characterized by increase in non-staphylococcus pathobionts and loss of specific species.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {23659},
pmid = {39390034},
issn = {2045-2322},
support = {HBC.2020.2873//Agentschap Innoveren en Ondernemen/ ; HBC.2020.2873//Agentschap Innoveren en Ondernemen/ ; 12S4222N//Fonds Wetenschappelijk Onderzoek/ ; 1S08523N//Fonds Wetenschappelijk Onderzoek/ ; 852600/ERC_/European Research Council/International ; },
mesh = {*Dermatitis, Atopic/microbiology ; Humans ; *Microbiota ; *Skin/microbiology/pathology ; Female ; Adult ; Male ; Staphylococcus aureus/genetics/isolation &amp; purification/pathogenicity ; Bacteria/classification/genetics ; Middle Aged ; Metagenomics/methods ; },
abstract = {Atopic dermatitis is the most common inflammatory skin condition with a severe negative impact on patients' quality of life. The etiology of AD is complex and depends on age, genetics, the immune system, environmental factors, and the skin microbiome, with a key role for pathogenic Staphylococcus aureus in the development of severe AD. However, the composition of the skin microbiome in mild AD is understudied. Here, using metagenomic shallow shotgun sequencing, we showed that mild AD lesions did not show a significant difference in the diversity of the skin microbiome compared to samples from non-AD patients and that the relative abundance of S. aureus did not differ in these mild AD lesions. However, when we assessed other taxa, Mycobacterium ostraviense, Pedobacter panaciterrae_A and four Streptomyces species were identified with higher abundances in mild AD lesions and species of 15 genera were decreased in abundance. The highest fold decreases were observed for Paracoccus marcusii, Microbacterium lacticum, Micrococcus luteus, and Moraxella sp002478835. These microbiome compositional insights are a first step towards novel microbiome-based diagnostics and therapeutics for early intervention at the stage of mild AD and provide a path forward for the functional study of species involved in this often-overlooked patient population.},
}
@article {pmid39387982,
year = {2024},
author = {Xing, F and Deng, C and Zou, S and Tsang, CC and Lo, SKF and Lau, SKP and Woo, PCY},
title = {Emergence and Rapid Diagnosis of Talaromyces marneffei Infections in Renal Transplant Recipients by Next-Generation Sequencing.},
journal = {Mycopathologia},
volume = {189},
number = {6},
pages = {91},
pmid = {39387982},
issn = {1573-0832},
support = {SZSM201911014//Sanming Project of Medicine in Shenzen Municipality/ ; MOE-112-S-023-A//Ministry of Education/ ; },
mesh = {Humans ; *Talaromyces/genetics/isolation &amp; purification ; *Kidney Transplantation/adverse effects ; *High-Throughput Nucleotide Sequencing ; Adult ; *Transplant Recipients ; *Mycoses/diagnosis/microbiology ; Male ; Metagenomics/methods ; China ; Bronchoalveolar Lavage Fluid/microbiology ; },
abstract = {In the last few years, next-generation sequencing (NGS) has emerged as a technology for laboratory diagnosis of many culture-negative infections and slow-growing microorganisms. In this study, we describe the use of metagenomic NGS (mNGS) for rapid diagnosis of T. marneffei infection in a 37-year-old renal transplant recipient who presented with chronic pneumonia syndrome. Bronchoalveolar lavage for mNGS was positive for T. marneffei sequence reads. Prolonged incubation of the bronchoalveolar lavage revealed T. marneffei colonies after 6 days of incubation. Analysis of 23 cases of T. marneffei infections in renal transplant recipients from the literature revealed that the number of cases ranged from 1 to 4 cases per five years from 1990 to 2020; but increased rapidly to 9 cases from 2021 to 2023, with 7 of them diagnosed by NGS. Twenty of the 23 cases were from T. marneffei-endemic areas [southern part of mainland China (n = 9); Hong Kong (n = 4); northeastern India (n = 2); Indonesia (n = 1) and Taiwan (n = 4)]. For the 3 patients from non-T. marneffei-endemic areas [United Kingdom (n = 2) and Australia (n = 1)], they had travel histories to China and Vietnam respectively. The time taken for diagnosis by mNGS [median 1 (range 1 to 2) day] was significantly shorter than that for fungal culture [median 6 (range 3 to 15) days] (P = 0.002). mNGS is useful for picking up more cases of T. marneffei infections in renal transplant recipients as well as providing a rapid diagnosis. Talaromycosis is an emerging fungal infection in renal transplant recipients.},
}
@article {pmid39390025,
year = {2024},
author = {Larsson, A and Ericson, U and Jönsson, D and Miari, M and Athanasiadis, P and Baldanzi, G and Brunkwall, L and Hellstrand, S and Klinge, B and Melander, O and Nilsson, PM and Fall, T and Maziarz, M and Orho-Melander, M},
title = {New connections of medication use and polypharmacy with the gut microbiota composition and functional potential in a large population.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {23723},
pmid = {39390025},
issn = {2045-2322},
mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; *Polypharmacy ; Male ; Female ; Middle Aged ; Sweden ; Aged ; Adult ; },
abstract = {Medication can affect the gut microbiota composition and function. The aim of this study was to investigate connections between use of common non-antibiotic medicines and the gut microbiota composition and function in a large Swedish cohort (N = 2223). Use of 67 medications and polypharmacy (≥ 5 medications), based on self-reported and prescription registry data, were associated with the relative abundance of 881 gut metagenomic species (> 5% prevalence) and 103 gut metabolic modules (GMMs). Altogether, 97 associations of 26 medications with 40 species and of four medications with five GMMs were observed (false discovery rate < 5%). Several earlier findings were replicated like the positive associations of proton pump inhibitors (PPIs) with numerous oral species, and those of metformin with Escherichia species and with lactate consumption I and arginine degradation II. Several new associations were observed between, among others, use of antidepressants, beta-blockers, nonsteroidal anti-inflammatory drugs and calcium channel blockers, and specific species. Polypharmacy was positively associated with Enterococcus faecalis, Bacteroides uniformis, Rothia mucilaginosa, Escherichia coli and Limosilactobacillus vaginalis, and with 13 GMMs. We confirmed several previous findings and identified numerous new associations between use of medications/polypharmacy and the gut microbiota composition and functional potential. Further studies are needed to confirm the new findings.},
}
@article {pmid39390011,
year = {2024},
author = {Kim, HS and Oh, SJ and Kim, BK and Kim, JE and Kim, BH and Park, YK and Yang, BG and Lee, JY and Bae, JW and Lee, CK},
title = {Dysbiotic signatures and diagnostic potential of gut microbial markers for inflammatory bowel disease in Korean population.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {23701},
pmid = {39390011},
issn = {2045-2322},
support = {2017R1A5A2014768//National Research Foundation of Korea/ ; 2021R1C1C2008556//National Research Foundation of Korea/ ; HI23C0661//Korea Health Industry Development Institute/Republic of Korea ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Dysbiosis/diagnosis/microbiology ; Female ; Male ; Republic of Korea/epidemiology ; Adult ; Middle Aged ; *Biomarkers ; *RNA, Ribosomal, 16S/genetics ; *Feces/microbiology ; *Inflammatory Bowel Diseases/microbiology/diagnosis ; Colitis, Ulcerative/microbiology/diagnosis ; Metagenomics/methods ; Crohn Disease/microbiology/diagnosis ; Case-Control Studies ; Cross-Sectional Studies ; Young Adult ; Aged ; },
abstract = {Fecal samples were collected from 640 individuals in Korea, including 523 patients with IBD (223 with Crohn's disease [CD] and 300 with ulcerative colitis [UC]) and 117 healthy controls. The samples were subjected to cross-sectional gut metagenomic analysis using 16 S rRNA sequencing and bioinformatics analysis. Patients with IBD, particularly those with CD, exhibited significantly lower alpha diversities than the healthy subjects. Differential abundance analysis revealed dysbiotic signatures, characterized by an expansion of the genus Escherichia-Shigella in patients with CD. Functional annotations showed that functional pathways related to bacterial pathogenesis and production of hydrogen sulfide (H2S) were strongly upregulated in patients with CD. A dysbiosis score, calculated based on functional characteristics, highly correlated with disease severity. Markers distinguishing between healthy subjects and patients with IBD showed accurate classification based on a small number of microbial taxa, which may be used to diagnose ambiguous cases. These findings confirm the taxonomic and functional dysbiosis of the gut microbiota in patients with IBD, especially those with CD. Taxa indicative of dysbiosis may have significant implications for future clinical research on the management and diagnosis of IBD.},
}
@article {pmid39389770,
year = {2024},
author = {Xu, Y and Yan, Y and Zhou, T and Lu, Y and Yang, X and Tang, K and Liu, F},
title = {Synergy between Arbuscular Mycorrhizal Fungi and Rhizosphere Bacterial Communities Increases the Utilization of Insoluble Phosphorus and Potassium in the Soil by Maize.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.4c07428},
pmid = {39389770},
issn = {1520-5118},
abstract = {Arbuscular mycorrhizal (AM) fungi can enhance plant uptake of phosphorus (P) and potassium (K), but it is not yet clear whether rhizosphere bacteria can enhance the ability of AM fungi to acquire insoluble P and K from the soil. Here, pot experiments confirmed that AM fungus-promoted insoluble P and K uptake by plants requires rhizosphere bacteria. The changes of rhizosphere bacterial communities associated with AM fungi were explored by 16S rRNA amplicon sequencing and metagenomic sequencing. Five core bacteria genera identified were involved in P and K cycles. Synthetic community (SynCom) inoculation revealed that SynCom increased soil available P and K and its coinoculation with AM fungi increased P and K concentration in the plants. This study revealed that AM fungi interact with rhizosphere bacteria and promote insoluble P and K acquisition, which provided a foundation for the application of AM fungal-bacterial biofertilizers and was beneficial for the sustainable development of agriculture.},
}
@article {pmid39389327,
year = {2024},
author = {Narain Singh, D and Pandey, P and Shankar Singh, V and Kumar Tripathi, A},
title = {Evidence for high-risk pollutants and emerging microbial contaminants at two major bathing ghats of the river Ganga using high-resolution mass spectrometry and metagenomics.},
journal = {Gene},
volume = {},
number = {},
pages = {148991},
doi = {10.1016/j.gene.2024.148991},
pmid = {39389327},
issn = {1879-0038},
abstract = {An efficient wastewater treatment plant is imperative to limit the entry of emerging pollutants (EPs) and emerging microbial contaminants (EMCs) in the river ecosystem. The detection of emerging EPs in aquatic environments is challenging due to complex sample preparation methods, and the need for sophisticated accurate analytical tools. In Varanasi (India), the river Ganga holds immense significance as a holy river but is consistently polluted with municipal (MWW) and hospital wastewater (HWW). We developed an efficient method for untargeted detection of EPs in the water samples using High-resolution mass spectrometry (HRMS), and identified 577 and 670 chemicals (or chemical components) in the water samples from two major bathing ghats, Assi Ghat (AG) and Dashashwamedh Ghat (DG), respectively. The presence of EPs of different categories viz chemicals from research labs, diagnostic labs, lifestyle and industrial chemicals, toxins, flavor and food additives indicated the unsafe disposal of MWW and HWW or inefficient wastewater treatment plants (WWTPs). Besides, shotgun metagenomic analysis depicted the presence of bacteria associated with MWW viz Cloacibacterium normanse, Sphaerotilus natans (sewage fungi), E. coli, and Prevotella. Also, the presence of human pathogens Arcobacter, Polynucleobacter, Pseudomonas, Klebsiella, Aeromonas, Acinetobacter, Vibrio, and Campylobacter suggests the discharge of HWW. EPs are linked to the development, and transmission of antimicrobial resistance (AMR). Occurrence of antibiotic resistance genes (ARGs), plasmid-borne β-lactamases, aminoglycoside transferases, and ARGs associated with integrons, transposons and plasmids viz mcr-3 gene that confer resistance to colistin, the last resort of antibiotics confirmed the presence of emerging microbial contaminants. Subsequent genome reconstruction studies showed the presence of uncultivable ARB and transmission of ARGs through horizontal gene transfer. This study can be used to monitor the health of aquatic bodies as well as the efficiency of WWTPs and raise an urgent need for efficient WWTPs to safeguard the river, Ganga.},
}
@article {pmid39389287,
year = {2024},
author = {Boycheva, S and Roberton, AM and Pisaniello, A and Pardesi, B and White, WL and Clements, KD},
title = {Oxygen exposure decreases the yield of high-molecular-weight DNA from some anaerobic bacteria and bacterial communities during DNA extraction.},
journal = {Anaerobe},
volume = {},
number = {},
pages = {102915},
doi = {10.1016/j.anaerobe.2024.102915},
pmid = {39389287},
issn = {1095-8274},
abstract = {OBJECTIVES: The central challenge in third-generation sequencing lies in meeting the requirements for DNA quality (integrity and purity) and quantity. Therefore, novel improvements in DNA extraction methods are needed to satisfy these requirements. We reasoned that in anaerobic microbial communities, the presence of certain strict anaerobes containing oxygen-activated DNase activity might contribute substantially to the poor integrity of extracted metagenomic DNA (or genomic DNA from some pure cultures) if exposed to air.<br><br>METHODS: To test this hypothesis, we developed an enhanced genomic and metagenomic DNA isolation technique that we applied to a specifically chosen set of both strict and aerotolerant anaerobes, as well as to the hindgut microbiota of an herbivorous marine fish.<br><br>RESULTS: Considering the quality (or degradation) of extracted DNA obtained under anaerobic versus aerobic conditions, we found that DNA extracted aerobically from cells of some strict anaerobes showed more degradation of high molecular weight DNA than analogous preparations under anaerobic conditions. In contrast, with the selected aerotolerant anaerobes, no discernable difference was found between the molecular sizes of DNA extracted aerobically and anaerobically. Metagenomic DNA extracted from the fish hindgut microbiota showed higher yields and better quality under anaerobic conditions compared to aerobic conditions.<br><br>CONCLUSION: Our study effectively demonstrates the advantages of our improved extraction protocol in anaerobic conditions. This is evident through the improved quality of extracted DNA. Such findings may be valuable for studies, especially metagenomic studies, where the quality and quantity of DNA are crucial for downstream analysis.},
}
@article {pmid39389249,
year = {2024},
author = {Lu, CW and Kao, CM and Yao, CL and Chen, SC},
title = {Analyzing Dehalochip: A Functional DNA Microarray for Reductive Dichlorination in Chloroethene-Contaminated Sites.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {125096},
doi = {10.1016/j.envpol.2024.125096},
pmid = {39389249},
issn = {1873-6424},
abstract = {Interpreting high-throughput transcriptomic and metagenomic data from non-model microorganisms presents a challenge due to the significant number of genes with unknown functions and sequences. In this study, we applied an innovative microarray, Dehalochip, for detecting the expression of genes in various microorganisms, particularly focusing on genes involved in chloroethene degradation. Our results demonstrated that this approach can effectively identify dechlorination genes, such as 16S rRNA, tceA, bvcA, and vcrA, in Dehalococcoides mccartyi from samples of groundwater contaminated with chloroethene. Noticeably, the sensitivity and specificity of our Dehalochip are comparable to that of quantitative PCR. However, it stands out as a more viable option for in-situ applications due to its greater capacity to infer potential dechlorination genes. Consequently, we believe our dechlorination microarray offers valuable insights into the role of known microorganisms and their associated functional genes in chloroethene-contaminated environments. This contributes to a deeper understanding of the in-situ reductive dechlorination process.},
}
@article {pmid39389057,
year = {2024},
author = {Hou, X and He, Y and Fang, P and Mei, SQ and Xu, Z and Wu, WC and Tian, JH and Zhang, S and Zeng, ZY and Gou, QY and Xin, GY and Le, SJ and Xia, YY and Zhou, YL and Hui, FM and Pan, YF and Eden, JS and Yang, ZH and Han, C and Shu, YL and Guo, D and Li, J and Holmes, EC and Li, ZR and Shi, M},
title = {Using artificial intelligence to document the hidden RNA virosphere.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2024.09.027},
pmid = {39389057},
issn = {1097-4172},
abstract = {Current metagenomic tools can fail to identify highly divergent RNA viruses. We developed a deep learning algorithm, termed LucaProt, to discover highly divergent RNA-dependent RNA polymerase (RdRP) sequences in 10,487 metatranscriptomes generated from diverse global ecosystems. LucaProt integrates both sequence and predicted structural information, enabling the accurate detection of RdRP sequences. Using this approach, we identified 161,979 potential RNA virus species and 180 RNA virus supergroups, including many previously poorly studied groups, as well as RNA virus genomes of exceptional length (up to 47,250 nucleotides) and genomic complexity. A subset of these novel RNA viruses was confirmed by RT-PCR and RNA/DNA sequencing. Newly discovered RNA viruses were present in diverse environments, including air, hot springs, and hydrothermal vents, with virus diversity and abundance varying substantially among ecosystems. This study advances virus discovery, highlights the scale of the virosphere, and provides computational tools to better document the global RNA virome.},
}
@article {pmid39389029,
year = {2024},
author = {Qian, J and Yeo, EN and Olm, MR},
title = {Hospitalization throws the preterm gut microbiome off-key.},
journal = {Cell host &amp; microbe},
volume = {32},
number = {10},
pages = {1651-1653},
doi = {10.1016/j.chom.2024.09.009},
pmid = {39389029},
issn = {1934-6069},
mesh = {*Gastrointestinal Microbiome ; Humans ; Infant, Newborn ; *Feces/microbiology ; *Intensive Care Units, Neonatal ; *Metagenomics ; *Infant, Premature ; Hospitalization ; Infant ; },
abstract = {Environmental exposures substantially influence the infant gut microbiome. In this issue of Cell Host &amp; Microbe, Thänert et al.[1] characterize how medical interventions in the neonatal intensive care unit (NICU) shape gut microbiome dynamics in the first months of life by analyzing over 2,500 fecal samples with metagenomics and metatranscriptomics.},
}
@article {pmid39388238,
year = {2024},
author = {Zhou, R and Hou, J and Fu, X and Wang, C and Liang, Y and Wang, D},
title = {A suprapubic refractory skin ulcer following keloid radiotherapy: from hyper-proliferation to hypo-proliferation.},
journal = {Journal of wound care},
volume = {33},
number = {Sup10},
pages = {S4-S8},
doi = {10.12968/jowc.2021.0314},
pmid = {39388238},
issn = {0969-0700},
mesh = {Humans ; Female ; Adult ; *Keloid/radiotherapy/etiology ; *Skin Ulcer/etiology ; Radiation Injuries/etiology ; Radiotherapy/adverse effects ; },
abstract = {Radiation-induced skin ulcer following cancer and/or tumour is well-documented in the literature. However, radiation-induced skin ulcer following the excision of keloid is yet to be reported. Here, we report the case of a 33-year-old female patient with a suprapubic skin ulcer of five months' duration following keloid treatment with electron beam therapy at recommended dosage. Various examinations, including a skin biopsy, metagenomic sequencing, magnetic resonance imaging and immunochemistry, indicated that the skin ulcer was induced by radiotherapy. While postoperative radiotherapy has been recommended immediately following keloid excision to reduce the risk of recurrence, the present case highlights the risk of skin refractory ulcer following keloid radiotherapy.},
}
@article {pmid39386812,
year = {2024},
author = {Cai, R and Yu, F and Cheng, J and Chen, C and Liu, Y and Lv, R and Ye, Z and Yuan, Y and Li, Z and Cheng, C and Wei, H},
title = {Diagnostic Value of Metagenomic next-generation sequencing and X-pert in Bronchoalveolar lavage fluid for pneumonia in HIV-infected and HIV-uninfected patients.},
journal = {Heliyon},
volume = {10},
number = {19},
pages = {e38208},
pmid = {39386812},
issn = {2405-8440},
abstract = {BACKGROUND: The pathogens causing unexplained pneumonia in both HIV-infected or HIV-unfected patients are likely to be complex. This retrospective study aimed to characterize the etiology of pneumonia in HIV-infected and HIV-uninfected patients using bronchoalveolar lavage fluid (BALF) analysis with metagenomic next-generation sequencing (mNGS) and X-pert MTB/RIF.<br><br>METHODS: Between January 2022 and May2024, 141 HIV-infected and 104 HIV-uninfected patients admitted to Nanjing Second Hospital with pneumonia were included. BALF samples were collected and analyzed using mNGS to detect bacteria, fungi, viruses, tuberculosis (TB) and non-tuberculous mycobacteria (NTM), and X-pert for TB detection. Clinical data including CD4 T-cell counts, comorbidities, and ART status were collected and analyzed.<br><br>RESULTS: HIV-uninfected patients were found to be older and exhibited a higher prevalence of comorbidities compared to HIV-infected patients. Despite higher median CD4 T-cell counts in HIV-uninfected individuals (412&#xa0;cells/&#x3bc;L vs. 31&#xa0;cells/&#x3bc;L in HIV-infected), TB detection rates using X-pert and mNGS were lower than anticipated, particularly in HIV-infected patients. Mixed-pathogen infections were significantly more prevalent in HIV-infected patients, especially those with lower CD4 T-cell counts. ART use showed variable impacts on pathogen diversity, with longer treatment durations associated with reduced infection complexity but persistent immunodeficiency in some cases.In patients with pneumonia, whether HIV-infected or HIV-uninfected, pathogens often exhibit complexity, underscoring the critical role of timely mNGS and X-pert analysis of BALF for early pathogen detection.},
}
@article {pmid39386754,
year = {2024},
author = {Wang, Q and Huang, Y and Ma, H and Fan, GK},
title = {A case report: Comorbidity of Rhinocerebral mucormycosis and pulmonary aspergillosis with challenging diagnosis.},
journal = {Frontiers in medicine},
volume = {11},
number = {},
pages = {1398714},
pmid = {39386754},
issn = {2296-858X},
abstract = {BACKGROUND: Mucormycosis is a rare opportunistic invasive fungal disease. Rhinocerebral mucormycosis (RCM) is clinically difficult to diagnose, and patients often die due to delayed diagnosis.<br><br>CASE DESCRIPTION: A patient with concurrent pulmonary aspergillosis was diagnosed with RCM caused by Rhizopus through metagenomic Next-Generation Sequencing (mNGS). Despite comprehensive treatment including surgery, amphotericin B, and posaconazole, the patient tragically passed away. The treatment was delayed due to repeated cultures of secretions were negative and pathological examination could not clarify which fungus is infected.<br><br>CONCLUSION: The clinical manifestations of RCM are not specific in the early stage, but the infection progresses rapidly. Therefore, early and accurate diagnosis is very important. mNGS is helpful for patients suspected of RCM, especially when conventional microbiology tests were negative.},
}
@article {pmid39386737,
year = {2024},
author = {Nunn, BL and Timmins-Schiffman, E and Mudge, MC and Plubell, D and Chebli, G and Kubanek, J and Riffle, M and Noble, WS and Harvey, E and Nunn, TA and Huntemann, M and Clum, A and Foster, B and Foster, B and Roux, S and Palaniappan, K and Mukherjee, S and Reddy, TBK and Daum, C and Copeland, A and Chen, IA and Ivanova, NN and Kyrpides, NC and Del Rio, TG and Eloe-Fadrosh, EA},
title = {Microbial Metagenomes Across a Complete Phytoplankton Bloom Cycle: High-Resolution Sampling Every 4 Hours Over 22 Days.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.09.27.614549},
pmid = {39386737},
issn = {2692-8205},
abstract = {In May and June of 2021, marine microbial samples were collected for DNA sequencing in East Sound, WA, USA every 4 hours for 22 days. This high temporal resolution sampling effort captured the last 3 days of a Rhizosolenia sp. bloom, the initiation and complete bloom cycle of Chaetoceros socialis (8 days), and the following bacterial bloom (2 days). Metagenomes were completed on the time series, and the dataset includes 128 size-fractionated microbial samples (0.22-1.2 µ m), providing gene abundances for the dominant members of bacteria, archaea, and viruses. This dataset also has time-matched nutrient analyses, flow cytometry data, and physical parameters of the environment at a single point of sampling within a coastal ecosystem that experiences regular bloom events, facilitating a range of modeling efforts that can be leveraged to understand microbial community structure and their influences on the growth, maintenance, and senescence of phytoplankton blooms.},
}
@article {pmid39386697,
year = {2024},
author = {Zelasko, S and Swaney, MH and Suh, WS and Sandstrom, S and Carlson, C and Cagnazzo, J and Golfinos, A and Fossen, J and Andes, D and Kalan, LR and Safdar, N and Currie, CR},
title = {Altered oral microbiota of drug-resistant organism carriers exhibit impaired gram-negative pathogen inhibition.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.09.24.614756},
pmid = {39386697},
issn = {2692-8205},
abstract = {The oral microbiome has been understudied as a reservoir for clinical pathogens, including drug-resistant strains. Understanding how alterations in microbiome functioning render this site vulnerable to colonization is essential, as multidrug-resistant organisms (MDRO) carriage is a major risk factor for developing serious infections. To advance our knowledge of oral MDRO carriage and protection against pathogen colonization conferred by native microbiota, we examined microbiomes from individuals colonized by MDROs (n=33) and non-colonized age-matched controls (n=30). Shotgun metagenomic analyses of oral swabs from study participants revealed significant differences in microbial communities with depletion of Streptococcus spp. among those colonized by multidrug-resistant gram-negative bacilli (RGNB), compared to non-carriers. We utilized metagenomic sequencing to characterize the oral resistome and find antimicrobial resistance genes are present in higher abundance among RNGB carriers versus non-carriers. High-throughput co-culture screening revealed oral bacteria isolated from MDRO non-carriers demonstrate greater inhibition of gram-negative pathogens, compared to isolates from carriers. Moreover, biosynthetic gene clusters from streptococci are found in higher abundance from non-carrier microbiomes, compared to RGNB carrier microbiomes. Bioactivity-guided fractionation of extracts from Streptococcus isolate SID2657 demonstrated evidence of strong E. coli and A. baumannii inhibition in a murine model of infection. Together, this provides evidence that oral microbiota shape this dynamic microbial community and may serve as an untapped source for much-needed antimicrobial small-molecules.},
}
@article {pmid39386638,
year = {2024},
author = {Liu, A and Tian, B and Qiu, C and Su, KJ and Jiang, L and Zhao, C and Song, M and Liu, Y and Qu, G and Zhou, Z and Zhang, X and Mungasavalli Gnanesh, SS and Thumbigere-Math, V and Luo, Z and Tian, Q and Zhang, LS and Wu, C and Ding, Z and Shen, H and Deng, HW},
title = {Multi-View Integrative Approach For Imputing Short-Chain Fatty Acids and Identifying Key factors predicting Blood SCFA.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.09.25.614767},
pmid = {39386638},
issn = {2692-8205},
abstract = {Short-chain fatty acids (SCFAs) are the main metabolites produced by bacterial fermentation of dietary fiber within gastrointestinal tract. SCFAs produced by gut microbiotas (GMs) are absorbed by host, reach bloodstream, and are distributed to different organs, thus influencing host physiology. However, due to the limited budget or the poor sensitivity of instruments, most studies on GMs have incomplete blood SCFA data, limiting our understanding of the metabolic processes within the host. To address this gap, we developed an innovative multi-task multi-view integrative approach (M [2] AE, Multi-task Multi-View Attentive Encoders), to impute blood SCFA levels using gut metagenomic sequencing (MGS) data, while taking into account the intricate interplay among the gut microbiome, dietary features, and host characteristics, as well as the nuanced nature of SCFA dynamics within the body. Here, each view represents a distinct type of data input (i.e., gut microbiome compositions, dietary features, or host characteristics). Our method jointly explores both view-specific representations and cross-view correlations for effective predictions of SCFAs. We applied M [2] AE to two in-house datasets, which both include MGS and blood SCFAs profiles, host characteristics, and dietary features from 964 subjects and 171 subjects, respectively. Results from both of two datasets demonstrated that M [2] AE outperforms traditional regression-based and neural-network based approaches in imputing blood SCFAs. Furthermore, a series of gut bacterial species (e.g., Bacteroides thetaiotaomicron and Clostridium asparagiforme), host characteristics (e.g., race, gender), as well as dietary features (e.g., intake of fruits, pickles) were shown to contribute greatly to imputation of blood SCFAs. These findings demonstrated that GMs, dietary features and host characteristics might contribute to the complex biological processes involved in blood SCFA productions. These might pave the way for a deeper and more nuanced comprehension of how these factors impact human health.},
}
@article {pmid39386242,
year = {2024},
author = {Zhang, R and Zhang, L and An, X and Li, J and Niu, C and Zhang, J and Geng, Z and Xu, T and Yang, B and Xu, Z and Yue, Y},
title = {Hybridization promotes growth performance by altering rumen microbiota and metabolites in sheep.},
journal = {Frontiers in veterinary science},
volume = {11},
number = {},
pages = {1455029},
pmid = {39386242},
issn = {2297-1769},
abstract = {Hybridization can substantially improve growth performance. This study used metagenomics and metabolome sequencing to examine whether the rumen microbiota and its metabolites contributed to this phenomenon. We selected 48 approximately 3 month-old male ♂Hu × ♀Hu (HH, n = 16), ♂Poll Dorset × ♀Hu (DH, n = 16), and ♂Southdown × ♀Hu (SH, n = 16) lambs having similar body weight. The sheep were fed individually under the same nutritional and management conditions for 95 days. After completion of the trial, seven sheep close to the average weight per group were slaughtered to collect rumen tissue and content samples to measure rumen epithelial parameters, fermentation patterns, microbiota, and metabolite profiles. The final body weight (FBW), average daily gain (ADG), and dry matter intake (DMI) values in the DH and SH groups were significantly higher and the feed-to-gain ratio (F/G) significantly lower than the value in the HH group; additionally, the papilla height in the DH group was higher than that in the HH group. Acetate, propionate, and total volatile fatty acid (VFA) concentrations in the DH group were higher than those in the HH group, whereas NH3-N concentration decreased in the DH and SH groups. Metagenomic analysis revealed that several Prevotella and Fibrobacter species were significantly more abundant in the DH group, contributing to an increased ability to degrade dietary cellulose and enrich their functions in enzymes involved in carbohydrate breakdown. Bacteroidaceae bacterium was higher in the SH group, indicating a greater ability to digest dietary fiber. Metabolomic analysis revealed that the concentrations of rumen metabolites (mainly lysophosphatidylethanolamines [LPEs]) were higher in the DH group, and microbiome-related metabolite analysis indicated that Treponema bryantii and Fibrobacter succinogenes were positively correlated with the LPEs. Moreover, we found methionine sulfoxide and N-methyl-4-aminobutyric acid were characteristic metabolites in the DH and SH groups, respectively, and are related to oxidative stress, indicating that the environmental adaptability of crossbred sheep needs to be further improved. These findings substantially deepen the general understanding of how hybridization promotes growth performance from the perspective of rumen microbiota, this is vital for the cultivation of new species and the formulation of precision nutrition strategies for sheep.},
}
@article {pmid39385283,
year = {2024},
author = {Li, Y and Chen, J and Lin, Y and Zhong, C and Jing, H and Liu, H},
title = {Thaumarchaeota from deep-sea methane seeps provide novel insights into their evolutionary history and ecological implications.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {197},
pmid = {39385283},
issn = {2049-2618},
mesh = {*Archaea/genetics/classification/metabolism ; *Methane/metabolism ; *Ammonia/metabolism ; *Phylogeny ; *Geologic Sediments/microbiology ; *Oxidation-Reduction ; *Seawater/microbiology ; Metagenomics ; Metagenome ; China ; Evolution, Molecular ; Nitrification ; },
abstract = {BACKGROUND: Ammonia-oxidizing archaea (AOA) of the phylum Thaumarchaeota mediate the rate-limiting step of nitrification and remove the ammonia that inhibits the aerobic metabolism of methanotrophs. However, the AOA that inhabit deep-sea methane-seep surface sediments (DMS) are rarely studied. Here, we used global DMS metagenomics and metagenome-assembled genomes (MAGs) to investigate the metabolic activity, evolutionary history, and ecological contributions of AOA. Expression of AOA-specific ammonia-oxidizing gene (amoA) was examined in the sediments collected from the South China Sea (SCS) to identify their active ammonia metabolism in the DMS.<br><br>RESULTS: Our analysis indicated that AOA contribute&#x2009;>&#x2009;75% to the composition of ammonia-utilization genes within the surface layers (above 30&#xa0;cm) of global DMS. The AOA-specific ammonia-oxidizing gene was actively expressed in the DMS collected from the SCS. Phylogenomic analysis of medium-/high-quality MAGs from 18 DMS-AOA indicated that they evolved from ancestors in the barren deep-sea sediment and then expanded from the DMS to shallow water forming an amoA-NP-gamma clade-affiliated lineage. Molecular dating suggests that the DMS-AOA origination coincided with the Neoproterozoic oxidation event (NOE), which occurred&#x2009;~&#x2009;800 million years ago (mya), and their expansion to shallow water coincided with the Sturtian glaciation (~&#x2009;713&#xa0;mya). Comparative genomic analysis suggests that DMS-AOA exhibit higher requirement of carbon source for protein synthesis with enhanced genomic capability for osmotic regulation, motility, chemotaxis, and utilization of exogenous organic compounds, suggesting it could be more heterotrophic compared with other lineages.<br><br>CONCLUSION: Our findings provide new insights into the evolutionary history of AOA within the Thaumarchaeota, highlighting their critical roles in nitrogen cycling in the global DMS ecosystems. Video Abstract.},
}
@article {pmid39385149,
year = {2024},
author = {Asao, K and Hashida, N and Maruyama, K and Motooka, D and Nakamura, S and Nishida, K},
title = {Cases of endophthalmitis caused by Candida albicans and Candida dubliniensis identified via internal transcribed spacer deep sequencing.},
journal = {BMC ophthalmology},
volume = {24},
number = {1},
pages = {444},
pmid = {39385149},
issn = {1471-2415},
support = {23K159060//Japan Society for the Promotion of Science/ ; 21K08505//Japan Society for the Promotion of Science/ ; },
mesh = {Humans ; *Endophthalmitis/microbiology/diagnosis ; Middle Aged ; Female ; *Eye Infections, Fungal/microbiology/diagnosis ; Male ; *Candidiasis/microbiology/diagnosis/drug therapy ; *High-Throughput Nucleotide Sequencing ; *Candida albicans/isolation &amp; purification/genetics ; *Candida/genetics/isolation &amp; purification ; DNA, Fungal/genetics ; Vitrectomy ; Antifungal Agents/therapeutic use ; Vitreous Body/microbiology ; },
abstract = {BACKGROUND: We report two cases of fungal endophthalmitis induced by Candida species identified based on internal transcribed spacer 1 (ITS1) sequencing.<br><br>CASE PRESENTATION: In two cases, endophthalmitis was suspected, and the patients underwent pars plana vitrectomy. Case 1 was a 64-year-old woman with a history of cataract surgery 10 days prior. She had a history of anal primary melanoma, which metastasized throughout the body and subsequently relapsed. Vitreous culture and ITS-1 deep sequencing revealed the presence of the rare fungus, Candida dubliniensis. Case 2 was a 54-year-old man with a history of liver cancer and kidney failure. Culture methods and ITS1 deep sequencing both revealed the presence of Candida albicans. Both patients exhibited good visual prognoses after treatment with topical and systemic antibiotics.<br><br>CONCLUSIONS: We present two cases of fungal endophthalmitis caused by two Candida species identified by both the culture method and ITS1 deep sequencing. The fungal pathogen was identified by ITS deep sequencing three days after sample submission; the culture method yielded results after 1 week. These findings support the applicability of ITS1 sequencing for timely pathogen identification for cases of fungal endophthalmitis and provide detailed taxonomic information at the species level.},
}
@article {pmid39385092,
year = {2024},
author = {Haverkamp, THA and Spilsberg, B and Johannessen, GS and Torp, M and Sekse, C},
title = {Detection and characterization of Campylobacter in air samples from poultry houses using shot-gun metagenomics - a pilot study.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {399},
pmid = {39385092},
issn = {1471-2180},
abstract = {BACKGROUND: Foodborne pathogens such as Campylobacter jejuni are responsible for a large proportion of the gastrointestinal infections worldwide associated with poultry meat. Campylobacter spp. can be found in the chicken fecal microbiome and can contaminate poultry meat during the slaughter process. Commonly used sampling methods to detect Campylobacter spp. at poultry farms use fecal droppings or boot swabs in combination with conventional culture techniques or PCR. In this pilot study, we have used air filtering and filters spiked with mock communities in combination with shotgun metagenomics to detect Campylobacter and test the applicability of this approach for the detection and characterization of foodborne pathogens. To the best of our knowledge is this the first study that combines air filtering with shotgun metagenomic sequencing for detection and characterization of Campylobacter.<br><br>RESULTS: Analysis of air filters spiked with different levels of Campylobacter, into a background of mock or poultry house communities, indicated that we could detect as little as 200 colony forming units (CFU) Campylobacter per sample using our protocols. The results indicate that even with limited sequencing effort we could detect Campylobacter in the samples analysed in this study. We observed significant amounts of Campylobacter in real-life samples from poultry houses using both real-time PCR as well as shotgun metagenomics, suggesting that the flocks in both houses were infected with Campylobacter spp. Interestingly, in both houses we find diverse microbial communities present in the indoor air which reflect the fecal microbiome of poultry. Some of the identified genera such as Staphylococcus, Escherichia and Pseudomonas are known to contain opportunistic pathogenic species.<br><br>CONCLUSIONS: These results show that air sampling of poultry houses in combination with shotgun metagenomics can detect and identify Campylobacter spp. present at low levels. This is important since early detection of Campylobacter enables measures to be put in place to ensure the safety of broiler products, animal health and public health. This approach has the potential to detect any pathogen present in poultry house air.},
}
@article {pmid39384811,
year = {2024},
author = {Devanga Ragupathi, NK and Muthuirulandi Sethuvel, DP and Ganesan, A and Murugan, D and Baskaran, A and Wannigama, DL and Monk, PN and Karunakaran, E and Veeraraghavan, B},
title = {Evaluation of mrkD, pgaC and wcaJ as biomarkers for rapid identification of K. pneumoniae biofilm infections from endotracheal aspirates and bronchoalveolar lavage.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {23572},
pmid = {39384811},
issn = {2045-2322},
support = {10065043//QR GCRF , UKRI/ ; GCRFNGR5\1293//Academy of Medical Sciences, UK/ ; },
mesh = {*Biofilms/growth &amp; development ; *Klebsiella pneumoniae/genetics/isolation &amp; purification ; Humans ; *Klebsiella Infections/microbiology/diagnosis ; *Biomarkers ; Bronchoalveolar Lavage Fluid/microbiology ; Bacterial Proteins/genetics ; },
abstract = {Klebsiella pneumoniae has been identified as one of the most important opportunistic pathogens responsible for nosocomial infections. Antibiotic resistance and the ability to form biofilms are the two main factors involved in the persistence of infections. Conventional detection methods involve culture isolation and identification followed by biofilm assay that takes 48-72 h. Timely detection of biofilm-forming resistant pathogens is essential to appropriately treat the infection with the right dose and combinations. The present study focuses on evaluating an RT-PCR panel using mrkD, pgaC, and wcaJ genes to screen for biofilm-forming K. pneumoniae from ETA/BAL specimens. The assay accurately identified K. pneumoniae harboring samples with a limit of detection of 1 ng/µl total RNA. Representative culture-negative-PCR-positive samples were subjected to metagenomics which identified K. pneumoniae reads in these samples confirming the specificity of RT-PCR. mrkD and pgaC act as K. pneumoniae specific identification whereas wcaJ acts as a negative marker for biofilm-forming K. pneumoniae. In addition, RT-PCR results correlated well with the phenotypic biofilm-forming assay. This RT-PCR assay is the first of its kind for rapid identification of biofilm-forming K. pneumoniae. The result of this study highlights that the rapid detection of K. pneumoniae biofilms based on the RT-PCR results coupled with clinical conditions would be appropriate to treat emerging infections or to prevent re-infections in clinical settings.},
}
@article {pmid39384807,
year = {2024},
author = {Minot, SS and Li, N and Srinivasan, H and Ayers, JL and Yu, M and Koester, ST and Stangis, MM and Dominitz, JA and Halberg, RB and Grady, WM and Dey, N},
title = {Colorectal cancer-associated bacteria are broadly distributed in global microbiomes and drivers of precancerous change.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {23646},
pmid = {39384807},
issn = {2045-2322},
support = {K08 DK111941/DK/NIDDK NIH HHS/United States ; U54 CA274374/CA/NCI NIH HHS/United States ; R50CA233042//U.S. Department of Health and Human Services | NIH | National Cancer Institute (NCI)/ ; },
mesh = {*Colorectal Neoplasms/microbiology/genetics ; *Gastrointestinal Microbiome/genetics ; Animals ; Humans ; Mice ; *Bacteria/genetics/classification ; *Precancerous Conditions/microbiology ; Metagenomics/methods ; },
abstract = {The gut microbiome is implicated in the pathogenesis of colorectal cancer (CRC), but the full scope of this dialogue is unknown. Here we aimed to define the scale and membership of the body of CRC- and health-associated gut bacteria in global populations. We performed a microbiome-CRC correlation analysis of published ultra-deep shotgun metagenomic sequencing data from global microbiome surveys, utilizing a de novo (reference-agnostic) gene-level clustering approach to identify protein-coding co-abundant gene (CAGs) clusters. We link an unprecedented ~ 23-40% of gut bacteria to CRC or health, split nearly evenly as CRC- or health-associated. These microbes encode 2319 CAGs encompassing 427,261 bacterial genes significantly enriched or depleted in CRC. We identified many microbes that had not previously been linked to CRC, thus expanding the scope of "known unknowns" of CRC-associated microbes. We performed an agnostic CAG-based screen of bacterial isolates and validated predicted effects of previously unimplicated bacteria in preclinical models, in which we observed differential induction of precancerous adenomas and field effects. Single-cell RNA sequencing disclosed microbiome-induced senescence-associated gene expression signatures in discrete colonic populations including fibroblasts. In organoid co-cultures, primary colon fibroblasts from mice with microbiomes promoted significantly greater growth than fibroblasts from microbiome-depleted mice. These results offer proof-of-principle for gene-level metagenomic analysis enabling discovery of microbiome links to health and demonstrate that the microbiome can drive precancer states, thereby potentially revealing novel cancer prevention opportunities.},
}
@article {pmid39384533,
year = {2024},
author = {Vuillemin, A and Ruiz-Blas, F and Yang, S and Bartholomäus, A and Henny, C and Kallmeyer, J},
title = {Taxonomic and functional partitioning of Chloroflexota populations under ferruginous conditions at and below the sediment-water interface.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiae140},
pmid = {39384533},
issn = {1574-6941},
abstract = {The adaption of the phylum Chloroflexota to various geochemical conditions is thought to have originated in primitive microbial ecosystems, involving hydrogenotrophic energy conservation under ferruginous anoxia. Oligotrophic deep waters displaying anoxic ferruginous conditions, such as those of Lake Towuti, and their sediments may thus constitute a preferential ecological niche for investigating metabolic versatility in modern Chloroflexota. Combining pore water geochemistry, cell counts, sulfate reduction rates, 16S rRNA genes with in-depth analysis of metagenome-assembled genomes, we show that Chloroflexota benefit from cross-feeding on metabolites derived from canonical respiration chains and fermentation. Detailing their genetic contents, we provide molecular evidence that Anaerolineae have metabolic potential to use unconventional electron acceptors, different cytochromes and multiple redox metalloproteins to cope with oxygen fluctuations, and thereby effectively colonizing the ferruginous sediment-water interface. In sediments, Dehalococcoidia evolved to be acetogens, scavenging fatty acids, haloacids and aromatic acids, apparently bypassing specific steps in carbon assimilation pathways to perform energy-conserving secondary fermentations combined with CO2 fixation via the Wood-Ljungdahl pathway. Our study highlights the partitioning of Chloroflexota populations according to alternative electron acceptors and donors available at the sediment-water interface and below. Chloroflexota would have developed analogous primeval features due to oxygen fluctuations in ancient ferruginous ecosystems.},
}
@article {pmid39384050,
year = {2024},
author = {Wu, H and Yu, Y and Su, Q and Zhang, TC and Du, D and Du, Y},
title = {Combined impact of antibiotics and Cr(VI) on antibiotic resistance, ARGs, and growth of Bacillussp. SH-1: A functionl analysis from gene to protease.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {131579},
doi = {10.1016/j.biortech.2024.131579},
pmid = {39384050},
issn = {1873-2976},
abstract = {The simultaneous selection of antibiotic resistance genes (ARGs) induced by heavy metals and antibiotics has emerged as a growing environmental problem. This study investigated the combined effects of chromium (Cr(VI)) and antibiotics on the ARGs of Bacillus cereus SH-1. As Cr(VI) concentration increased, it triggered reactive oxygen species oxidative stress in SH-1, increased antioxidant enzyme activity, enhanced plasmid conjugative transfer, and reduced the efficiency of Cr(VI) removal by SH-1. Antibiotic resistance varied with increasing tetracycline and amoxicillin minimum inhibitory concentrations (MICs), whereas azithromycin and chloramphenicol MICs decreased with Cr(VI) induction. The overexpression of eight genes of the HAE-1 family of efflux pumps was detected using metagenomics and proteomics. Co-contamination with Cr(VI) and antibiotics has led to the emergence and spread of antibiotic-resistant bacteria. Therefore, resistance gene contamination resulting from Cr(VI)-polluted environments cannot be overlooked.},
}
@article {pmid39383807,
year = {2024},
author = {Zhang, Q and Ji, XM and Wang, X and Wang, W and Xu, X and Zhang, Q and Xing, D and Ren, N and Lee, DJ and Chen, C},
title = {Differentiation of the Anammox core microbiome: Unraveling the evolutionary impetus of scalable gene flow.},
journal = {Water research},
volume = {268},
number = {Pt A},
pages = {122580},
doi = {10.1016/j.watres.2024.122580},
pmid = {39383807},
issn = {1879-2448},
abstract = {Anaerobic ammonium oxidation bacteria (AAOB), distinguished by their unique autotrophic nitrogen metabolism, hold pivotal positions in the global nitrogen cycle and environmental biotechnologies. However, the ecophysiology and evolution of AAOB remain poorly understood, attributed to the absence of monocultures. Hence, a comprehensive elucidation of the AAOB-dominated core microbiome, anammox core, is imperative to further completing the theory of engineered nitrogen removal and ecological roles of anammox. Performing taxonomic and phylogenetic analyses on collected genome repertoires, we show here that Candidatus Brocadia and Candidatus Kuenenia possesses a more compact core than Candidatus Jettenia, which partly explains why the latter has a less common ecological presence. Evidence of gene flow is particularly striking in functions related to biosynthesis and oxygen detoxification, underscoring the evolutionary forces driving lineage and core differentiation. Furthermore, CRISPR spacer traceback of the AAOB metagenome-assembled genomes (MAGs) reveals a series of genetic traces for the concealed phages. By reconceptualizing the functional divergence of AAOB with the historical role of phages, we ultimately propose a coevolutionary framework to understand the evolutionary trajectory of anammox microecology. The discoveries provided in this study offer new insights into understanding the evolution of AAOB and the ecology of anammox.},
}
@article {pmid39383805,
year = {2024},
author = {Trinh, HP and Lee, SH and Kim, NK and Nguyen, TV and Park, HD},
title = {Fimbriimonadales performed dissimilatory nitrate reduction to ammonium (DNRA) in an anammox reactor.},
journal = {Water research},
volume = {268},
number = {Pt A},
pages = {122575},
doi = {10.1016/j.watres.2024.122575},
pmid = {39383805},
issn = {1879-2448},
abstract = {Bacteria belonging to the order Fimbriimonadales are frequently detected in anammox reactors. However, the principal functions of these bacteria and their potential contribution to nitrogen removal remain unclear. In this study, we aimed to systematically validate the roles of Fimbriimonadales in an anammox reactor fed with synthetic wastewater. High-throughput 16S rRNA gene sequencing analysis revealed that heterotrophic denitrifying bacteria (HDB) were the most abundant bacterial group at the initial stage of reactor operation and the abundance of Fimbriimonadales members gradually increased to reach 38.8 % (day 196). At the end of reactor operation, Fimbriimonadales decreased to 0.9 % with an increase in anammox bacteria. Correlation analysis demonstrated nitrate competition between Fimbriimonadales and HDB during reactor operation. Based on the phylogenetic analysis, the Fimbriimonadales sequences acquired from the reactor were clustered into three distinct groups, which included the sequences obtained from other anammox reactors. Metagenome-assembled genome analysis of Fimbriimonadales allowed the identification of the genes narGHI and nrfAH, responsible for dissimilatory nitrate reduction to ammonium (DNRA), and nrt and nasA, responsible for nitrate and nitrite transport. In a simulation based on mass balance equations and quantified bacterial groups, the total nitrogen concentrations in the effluent were best predicted when Fimbriimonadales was assumed to perform DNRA (R[2] = 0.70 and RMSE = 18.9). Moreover, mass balance analysis demonstrated the potential contribution of DNRA in enriching anammox bacteria and promoting nitrogen removal. These results prove that Fimbriimonadales compete with HDB for nitrate utilization through DNRA in the anammox reactor under non-exogenous carbon supply conditions. Overall, our findings suggest that the DNRA pathway in Fimbriimonadales could enhance anammox enrichment and nitrogen removal by providing substrates (nitrite and/or ammonium) for anammox bacteria.},
}
@article {pmid39383803,
year = {2024},
author = {Xiang, Y and Song, X and Yang, Y and Deng, S and Fu, L and Yang, C and Chen, M and Pu, J and Zhang, H and Chai, H},
title = {Comammox rather than AOB dominated the efficient autotrophic nitrification-denitrification process in an extremely oxygen-limited environment.},
journal = {Water research},
volume = {268},
number = {Pt A},
pages = {122572},
doi = {10.1016/j.watres.2024.122572},
pmid = {39383803},
issn = {1879-2448},
abstract = {The discovery of complete ammonia oxidizer (comammox) has challenged the traditional understanding of the two-step nitrification process. However, their functions in the oxygen-limited autotrophic nitrification-denitrification (OLAND) process remain unclear. In this study, OLAND was achieved using comammox-dominated nitrifying bacteria in an extremely oxygen-limited environment with a dissolved oxygen concentrations of 0.05 mg/L. The ammonia removal efficiency exceeded 97 %, and the total nitrogen removal efficiency reached 71 % when sodium bicarbonate was used as the carbon source. The pseudo-first- and second-order models were found to best fit the ammonia removal processes under low and high loads, respectively, suggesting distinct ammonia removal pathways. Full-length 16S rRNA gene sequencing and metagenomic results revealed that comammox-dominated under different oxygen levels, in conjunction with anammox and heterotrophic denitrifiers. The abundance of enzymes involved in energy metabolism indicates the coexistence of anammox and autotrophic nitrification-heterotrophic denitrification pathways. The binning results showed that comammox bacteria engaged in horizontal gene transfer with nitrifiers, anammox bacteria, and denitrifiers to adapt to an obligate environments. Therefore, this study demonstrated that comammox, anammox, and heterotrophic denitrifiers play important roles in the OLAND process and provide a reference for further reducing aeration energy in the autotrophic nitrogen removal process.},
}
@article {pmid39383762,
year = {2024},
author = {Serrano-Blanco, S and Zan, R and Harvey, AP and Velasquez-Orta, SB},
title = {Intensified microalgae production and development of microbial communities on suspended carriers and municipal wastewater.},
journal = {Journal of environmental management},
volume = {370},
number = {},
pages = {122717},
doi = {10.1016/j.jenvman.2024.122717},
pmid = {39383762},
issn = {1095-8630},
abstract = {Wastewater represents an alternative source of nutrients in which to grow microalgae, whilst improving the quality of the wastewater, and reducing the downstream treatment required. However, commercialisation of microalgal cultures for such duties faces a number of challenges, predominantly high cost and low productivity. Suspended-solid reactors (ssPBR) can reduce the operational costs, while promoting attached and suspended microalgae growth. In the present study, a novel approach was developed by integrating microalgal wastewater treatment with carrier systems to favour the growth of both attached and suspended cells of T. obliquus. This study found that T. obliquus was able to uptake nutrients from municipal wastewater, achieving removals of 99.3-99.9 % NH3-N, 54.5-88.5 % PO4[3-] and 92.8-94.5 % DTC. The addition of a 12.5 % volumetric fill ratio of carriers in ssPBRs produced higher microalgal cell productivity (1.2·10[6] ± 2.5·10[5] cell ml[-1] d[-1]) than the control (4.3·10[5] ± 2.8·10[5] cell ml[-1] d[-1]). MinION nanopore sequencing was conducted to assess the impact of microalgal and carrier treatment on wastewater bacterial communities. It was found not only that bacterial communities had changed after the treatment but also the ones attached differed from the ones suspended. Untreated wastewater was characterised by the abundance of sewer bacteria genera such as Aliarcobacter and Arcobacter, whilst, after treatment, microbial communities were characterised by the presence of photosynthetic freshwater (Limnococcus, Stanieria) and bioremediation-like bacteria genera (Pseudomonas, Rheinheimera). In conclusion, the addition of 12.5 % fill carrier ratio increased microalgal productivity, while stimulating changes in the algal microbiome, and creating distinctly different populations in the free and attached environments.},
}
@article {pmid39383754,
year = {2024},
author = {Wu, Y and Sun, Q and Zhou, Z and Wang, Z and Fu, H},
title = {Efficient degradation of carbamazepine and metagenomic investigations of anodic biofilm in microbial fuel cells.},
journal = {Journal of environmental management},
volume = {370},
number = {},
pages = {122743},
doi = {10.1016/j.jenvman.2024.122743},
pmid = {39383754},
issn = {1095-8630},
abstract = {Environmental contamination with carbamazepine is a considerable global problem. In this study, two-compartment microbial fuel cells (MFCs) were constructed to investigate the degradation performance of carbamazepine, and the degradation mechanism was further explored by using metagenomic analysis. The results showed that MFCs exhibited excellent carbamazepine removal performance and also generated electricity. The removal rate of carbamazepine reached 73.56% over the 72-h operation period, which was 3.09 times higher than that of the traditional anaerobic method, and the peak voltage of the MFCs could reach 416 mV. Metagenomics revealed significant differences in microbial community composition between MFCs and the traditional anaerobic method (p < 0.05), and Proteobacteria (81.57%) was predominant bacterial phyla during the degradation of carbamazepine by MFCs. Among them, the microbial communities at the genus level were mainly composed of Pseudomonas, Pusillimonas, Burkholderia, Stenotrophomonas, Methyloversatilis and Nitrospirillum. Kyoto Encyclopedia of genes and genomes (KEGG) metabolic pathway analysis showed that the number of genes related to carbon and nitrogen metabolism increased by 85.12% and 142.25%, respectively. Importantly, a greater number of genes of microbial grown on the surface of anode were assigned to denitrification and the degradation of aromatic compounds. This research provides a cost-effective method for treating wastewater contaminated with carbamazepin.},
}
@article {pmid39383151,
year = {2024},
author = {Xing, F and Deng, C and Huang, J and Yuan, Y and Luo, Z and Lo, SKF and Lau, SKP and Woo, PCY},
title = {Usefulness of next-generation sequencing for laboratory diagnosis of rickettsiosis.},
journal = {PLoS neglected tropical diseases},
volume = {18},
number = {10},
pages = {e0012546},
doi = {10.1371/journal.pntd.0012546},
pmid = {39383151},
issn = {1935-2735},
mesh = {Humans ; Female ; Male ; *Rickettsia Infections/diagnosis/microbiology ; *High-Throughput Nucleotide Sequencing/methods ; Middle Aged ; *Rickettsia/genetics/isolation &amp; purification ; Aged ; Metagenomics/methods ; Adult ; Orientia tsutsugamushi/genetics/isolation &amp; purification ; Scrub Typhus/diagnosis/microbiology ; Molecular Diagnostic Techniques/methods ; },
abstract = {Rickettsiosis includes a diversity of culture-negative non-specific systemic infections. Laboratory diagnosis of rickettsiosis is often not easy. In this 12-month study, six patients with a variety of rickettsia infections of the spotted fever group, typhus group and scrub typhus were diagnosed directly or indirectly by metagenomic next-generation sequencing (mNGS). The patient with Japanese spotted fever was rapidly made when mNGS analysis of the patient's blood revealed Rickettsia japonica sequences. For the two patients with Rickettsia felis chest infections, the bacterium was detected in the bronchoalveolar lavage of one case and lung biopsy of the other. Both patients had underlying malignancies, carcinoma of the breast and carcinoma of the lung respectively, and were on chemotherapy with immunosuppressive effect. For the remaining three patients who presented over a period of 13 weeks, all had fever, headache and the typical eschar. They also had increased serum transaminases and responded promptly to doxycycline. However, the Weil-Felix test results of all three patients were negative. Since we considered the three cases typical of rickettsiosis, we submitted their serum samples for mNGS analysis. Results showed that Orientia tsutsugamushi sequences were present in the serum of one case. In view of the positive mNGS results, we repeated the Weil-Felix test for the residual sera of all three patients and it revealed that those of the other two cases showed OX-19 titers of 1:640 and 1:160 respectively, inferring that these two patients probably had rickettsiosis of the typhus group. As for the patient positive for O. tsutsugamushi sequences, we also detected IgM for O. tsutsugamushi in the serum, which double confirmed that it was a case of scrub typhus. mNGS is an important molecular tool and can complement serology for laboratory diagnosis of rickettsiosis.},
}
@article {pmid39382920,
year = {2024},
author = {Zhang, L and Sun, SY and Yao, XX and Fu, AS and Ge, YL},
title = {Non-Tuberculous Mycobacterial Pulmonary Disease with Detection of Mycobacterium Tuberculosis in Pleural Fluid.},
journal = {Clinical laboratory},
volume = {70},
number = {10},
pages = {},
doi = {10.7754/Clin.Lab.2024.240531},
pmid = {39382920},
issn = {1433-6510},
mesh = {Humans ; *Mycobacterium Infections, Nontuberculous/diagnosis/microbiology ; *Mycobacterium tuberculosis/isolation &amp; purification/genetics ; *Pleural Effusion/microbiology/diagnosis ; Male ; High-Throughput Nucleotide Sequencing ; Antitubercular Agents/therapeutic use ; Middle Aged ; Female ; Tomography, X-Ray Computed/methods ; Tuberculosis, Pleural/diagnosis/microbiology/drug therapy ; },
abstract = {BACKGROUND: Tuberculous pleurisy (TP) is one of the most common types of extrapulmonary tuberculosis, often secondary to tuberculosis (TB). Clinical and imaging manifestations of non-tuberculous mycobacterial pulmonary diseases (NTM-PD) are usually similar to those of tuberculosis. Because of their similarity and the high incidence of tuberculosis, non-tuberculous mycobacterial infections are often overlooked for a long time. Especially in people without immunodeficiency.<br><br>METHODS: Mycobacterium tuberculosis (MTB) in pleural effusion was found by metagenomic next-generation sequencing (mNGS). During anti-tuberculosis treatment, mNGS of lung tissue by ultrasound-guided percutaneous lung puncture revealed that this patient had combined NTM-PD.<br><br>RESULTS: Mycobacterium chelonae (M. chelonae) was detected by mNGS, and after anti-NTM treatment, the patient's chest CT showed that the inflammation was absorbed more than before, and the patient's symptoms improved.<br><br>CONCLUSIONS: When TB is poorly treated with standardized anti-tuberculosis therapy, comorbid non-tuberculous mycobacterial infections may be considered, and mNGS may complement traditional pathogenetic testing.},
}
@article {pmid39382160,
year = {2024},
author = {Xue, S and Yi, X and Peng, J and Bak, F and Zhang, L and Duan, G and Liesack, W and Zhu, Y},
title = {Fulvic Acid Enhances Nitrogen Fixation and Retention in Paddy Soils through Microbial-Coupled Carbon and Nitrogen Cycling.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c07616},
pmid = {39382160},
issn = {1520-5851},
abstract = {Fulvic acid, the most soluble and active humic substance, is widely used as an agent to remediate contaminated soils and improve soil fertility. However, the influence of fulvic acid (FA), as a microbial carbon source, on carbon and nitrogen cycles in paddy soils remains elusive. Therefore, to investigate it, an incubation experiment was conducted. Gas analyses indicated that the carbon dioxide and methane emissions were enhanced in FA treatment, which increased up to 94.08-fold and 5.06-fold, respectively. [15]N-labeling experiments revealed that nitrogen fixation capability was promoted (1.2-fold) to reduce the carbon and nitrogen imbalance due to fulvic acid amendment. Metagenomic analysis further revealed that gene abundances of degradation of lignin-like compounds, gallate degradation, methanogenesis, nitrogen fixation, and urea hydrolysis increased, while the bacterial ammonia oxidation and anaerobic ammonium oxidation decreased, caused by FA application. Metabolic reconstruction of metagenome-assembled genomes revealed that Azospirillaceae, Methanosarcinaceae, and Bathyarchaeota, with higher abundance in FA treatment, were the key microorganisms to maintain the carbon and nitrogen balance. The metabolic pathways of fulvic acid degradation and coupled nitrogen fixation and retention were constructed. Collectively, our results provided novel insights into the theoretical basis of the use of humic substances for reducing nitrogen fertilization and climate change.},
}
@article {pmid39382010,
year = {2024},
author = {Wang, J and Fan, S and He, J and Jiang, X and Lin, R and Ji, Y and Ge, Y},
title = {A case report of fatal Rickettsia japonica bloodstream infection in Zhejiang, China.},
journal = {Future microbiology},
volume = {},
number = {},
pages = {1-6},
doi = {10.1080/17460913.2024.2406122},
pmid = {39382010},
issn = {1746-0921},
abstract = {Japanese spotted fever (JSF) is an emerging acute febrile natural infectious disease caused by the neglected zoonotic pathogen Rickettsia japonica. Here we reported a 64-year-old female patient who initially presented to the local hospital with an intermittent fever of unknown origin (FUO). A systemic, evident edema and eschar on the skin of the patient's upper limb was observed. The patient was diagnosed with critical Rickettsia japonica bloodstream infection by Q-mNGS and treated with doxycycline, as well as symptomatic treatments. Unfortunately, the patient passed away as a result of complications of septic shock and multiple organ and acute respiratory failure. Delayed treatment resulting from the nonspecific clinical symptoms in the early stages of infection can lead to fatal complications. Q-mNGS is an emerging pathogen detection method with the advantages of comprehensive detection, high accuracy and sensitivity and should be promoted and applied by clinicians.},
}
@article {pmid39381854,
year = {2024},
author = {Drahun, I and Morrison, K and Poole, EA and van Herk, WG and Cassone, BJ},
title = {Characterisation of the bacteriomes harboured by major wireworm pest species in the Canadian Prairies.},
journal = {Insect molecular biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/imb.12962},
pmid = {39381854},
issn = {1365-2583},
support = {RGPIN-2016-04335//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN-2023-04126//Natural Sciences and Engineering Research Council of Canada/ ; //Brandon University Research Committee/ ; },
abstract = {Nearly all insects harbour bacterial communities that can have a profound effect on their life history, including regulating and shaping host metabolism, development, immunity and fitness. The bacteriomes of several coleopterans have been described; however, very little has been reported for wireworms. These long-lived larvae of click beetles (Coleoptera: Elateridae) are major agricultural pests of a variety of crops grown in the Canadian Prairies. Consequently, the goal of this study was to characterise the bacteriomes of five of the most significant pest species within the region: Limonius californicus, Hypnoidus abbreviatus, H. bicolor, Aeolus mellillus and Dalopius spp. To do this, we collected larvae from southern Manitoba fields (pre-seeding) and carried out 16S rRNA sequencing on individual specimens. Our results indicate wireworms have diverse and taxon-rich bacterial communities, with over 400 genera identified predominately from the phyla Proteobacteria, Actinobacteriota, Bacteroidota and Firmicutes. However, each species had nine or fewer genera comprising >80% of their bacteriome. Network analyses revealed some community structuring consistent among species, which may culminate in shaping/regulating host biology. Moreover, the microbial signatures were influenced by both ontogeny (early vs. late stage larvae) and reproductive strategy (sexual vs. parthenogenetic), with a myriad of other factors likely contributing to bacterial diversity that are impossible to resolve from our study. Overall, this metagenomics study represents the first to characterise the bacteriomes of wireworms in the Canadian Prairies and the findings could assist in the development of sustainable management strategies for these important agricultural pests.},
}
@article {pmid39381756,
year = {2024},
author = {Sun, Y and Zhang, C and Lu, B and Chen, J and Pan, X},
title = {Case report: Mycobacterium chimaera-induced lymph node infection in a patient with chronic myeloproliferative neoplasm misdiagnosed as tuberculous lymphadenitis.},
journal = {Frontiers in public health},
volume = {12},
number = {},
pages = {1387722},
pmid = {39381756},
issn = {2296-2565},
mesh = {Humans ; Female ; Middle Aged ; *Tuberculosis, Lymph Node/diagnosis/drug therapy ; *Diagnostic Errors ; *Mycobacterium/isolation &amp; purification ; Lymphadenitis/microbiology/diagnosis ; Mycobacterium Infections, Nontuberculous/diagnosis/drug therapy ; Lymph Nodes/pathology/microbiology ; Myeloproliferative Disorders/diagnosis ; },
abstract = {Herein, we report a case of lymphadenitis caused by Mycobacterium chimaera. A 54-year-old woman with chronic myeloproliferative neoplasm was admitted to the hospital with cervical lymphadenopathy. After preliminary exclusion of various diseases such as lymphoma, Epstein-Barr virus infection, and autoimmune disease, a lymph node biopsy specimen showed epithelioid granulomatous lymphadenitis with caseous necrosis, epithelial-like cells, and multinucleated giant cells as seen in tuberculosis (TB). Although Mycobacterium tuberculosis was never isolated, diagnostic anti-TB treatment was commenced. Following over 9 months of treatment, there was no significant reduction in the size of her cervical lymph nodes, and she continued to experience recurrent low-grade fevers. One sample from the fourth lymph node biopsy tested negative for metagenomic next-generation sequencing (mNGS), and another sample tested positive in the BACTEC MGIT960 liquid culture system, identifying the strains as Mycobacterium chimaera. Anti-non-tuberculous mycobacteria (NTM) therapy was initiated, and the patient achieved symptom improvement. In conclusion, NTM lymphoid infection is easily misdiagnosed as long-term etiologic negativity.},
}
@article {pmid39381141,
year = {2024},
author = {Luo, Q and Lu, M and Butt, H and Lytal, N and Du, R and Jiang, H and An, L},
title = {TimeNorm: a novel normalization method for time course microbiome data.},
journal = {Frontiers in genetics},
volume = {15},
number = {},
pages = {1417533},
pmid = {39381141},
issn = {1664-8021},
abstract = {Metagenomic time-course studies provide valuable insights into the dynamics of microbial systems and have become increasingly popular alongside the reduction in costs of next-generation sequencing technologies. Normalization is a common but critical preprocessing step before proceeding with downstream analysis. To the best of our knowledge, currently there is no reported method to appropriately normalize microbial time-series data. We propose TimeNorm, a novel normalization method that considers the compositional property and time dependency in time-course microbiome data. It is the first method designed for normalizing time-series data within the same time point (intra-time normalization) and across time points (bridge normalization), separately. Intra-time normalization normalizes microbial samples under the same condition based on common dominant features. Bridge normalization detects and utilizes a group of most stable features across two adjacent time points for normalization. Through comprehensive simulation studies and application to a real study, we demonstrate that TimeNorm outperforms existing normalization methods and boosts the power of downstream differential abundance analysis.},
}
@article {pmid39381012,
year = {2024},
author = {Babalola, OO and Molefe, RR and Amoo, AE},
title = {Metagenome assembly and annotation of data from the rhizosphere soil of drought-stressed CRN-3505 maize cultivar.},
journal = {Data in brief},
volume = {57},
number = {},
pages = {110966},
pmid = {39381012},
issn = {2352-3409},
abstract = {This data article reports shotgun metagenomic data obtained from drought-stressed maize rhizosphere through the Illumina Novaseq platform, utilizing the KBase online platform. 428,339,852 high-quality post-sequences were obtained, showcasing an average GC content of 65.45 %. The investigation, conducted at Molelwane farm in Mafikeng, South Africa, identified 13 metagenome-assembled genomes (MAGs). Functional annotation of these MAGs revealed their involvement in essential plant growth and development functions, such as sulfur and nitrogen metabolism. The dataset was deposited into the NCBI database, and MAGs accessions are available at DDBJ/ENA/GenBank under the accession number PRJNA101755.},
}
@article {pmid39381006,
year = {2024},
author = {Lalbiakmawia, B and Pulapet, S and Kathir, S and Lalengkimi, R and Markkandan, K and Chhandama, MVL and Nachimuthu, SK and Zothanzama, J},
title = {Dataset on bacterial diversity using 16S metagenome analysis in fermented rice beer from two breweries and grape wine of Mizoram, Northeast India.},
journal = {Data in brief},
volume = {57},
number = {},
pages = {110932},
pmid = {39381006},
issn = {2352-3409},
abstract = {The microbial diversity of fermented rice beer and grape wine in Mizoram was explored using 16S metagenome analysis. The collected samples were marked as C1 and B1 for fermented rice beer and D1 for grape wine. Next-generation sequencing of the 16S rRNA (V3-V4 region) was performed using the Illumina NovoSeq 6000 platform. Operational taxonomic units (OTUs) were identified with QIIME2, and statistical analyses were performed using R packages. The metagenome of the three samples comprised 464,826 raw reads that represented 116,206,500 base pairs and were clustered into 336 OTUs. The phylum Firmicutes was predominant in C1 (55 %), B1 (53 %) and D1 (52 %), respectively and biosysnthesis, pyruvate fermentation to be abundant functions. By applying 16S metagenome analysis, this data provide insights in to the complex community of bacteria involved in the fermentation process and their potential roles and interactions.},
}
@article {pmid39380680,
year = {2024},
author = {Karavaeva, V and Sousa, FL},
title = {Navigating the archaeal frontier: insights and projections from bioinformatic pipelines.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1433224},
pmid = {39380680},
issn = {1664-302X},
abstract = {Archaea continues to be one of the least investigated domains of life, and in recent years, the advent of metagenomics has led to the discovery of many new lineages at the phylum level. For the majority, only automatic genomic annotations can provide information regarding their metabolic potential and role in the environment. Here, genomic data from 2,978 archaeal genomes was used to perform automatic annotations using bioinformatics tools, alongside synteny analysis. These automatic classifications were done to assess how good these different tools perform in relation to archaeal data. Our study revealed that even with lowered cutoffs, several functional models do not capture the recently discovered archaeal diversity. Moreover, our investigation revealed that a significant portion of archaeal genomes, approximately 42%, remain uncharacterized. In comparison, within 3,235 bacterial genomes, a diverse range of unclassified proteins is obtained, with well-studied organisms like Escherichia coli having a substantially lower proportion of uncharacterized regions, ranging from <5 to 25%, and less studied lineages being comparable to archaea with the range of 35-40% of unclassified regions. Leveraging this analysis, we were able to identify metabolic protein markers, thereby providing insights into the metabolism of the archaea in our dataset. Our findings underscore a substantial gap between automatic classification tools and the comprehensive mapping of archaeal metabolism. Despite advances in computational approaches, a significant portion of archaeal genomes remains unexplored, highlighting the need for extensive experimental validation in this domain, as well as more refined annotation methods. This study contributes to a better understanding of archaeal metabolism and underscores the importance of further research in elucidating the functional potential of archaeal genomes.},
}
@article {pmid39380679,
year = {2024},
author = {Narenkumar, J and Das, B and Abilaji, S and Sathishkumar, K and AlSalhi, MS and Devanesan, S and Rajasekar, A and Malik, T},
title = {Biosurfactant-assisted bio-electrokinetic enhanced remediation of heavy metal-contaminated soil.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1458369},
pmid = {39380679},
issn = {1664-302X},
abstract = {BACKGROUND: Environmental soil contamination is a serious problem for humans worldwide, as it causes many diseases.<br><br>METHODS: The present study focuses on utilizing biosurfactants produced by Pseudomonas stutzeri (P. stutzeri) NA3 and Bacillus cereus (B. cereus) EN6, as an electrolyte for removing chromium (Cr) from contaminated soil using the electrokinetic (EK) process.<br><br>RESULTS: As a result, biosurfactants produced by P. stutzeri NA3 and B. cereus EN6, being lipopeptides, increase heavy metal mobility in the EK process. The Cr removal efficiency of a novel electrolyte (biosurfactants) in the EK process was compared with that of NA3 and EN6 biosurfactants. The EK results revealed a maximum Cr removal of 75 and 70% by NA3 and EN6, respectively, at the end of 7&#x2009;days.<br><br>DISCUSSION: The biosurfactant aids in the breaking down of the heavy metals that are present deeper into the soil matrix. From the metagenomics analysis, it was identified that biosurfactant changes the microbial community with an enhanced ability to remove heavy metals. The phytotoxicity assay confirms that NA3 biosurfactant solution showed 95% seed germination and can lower hazardous pollutants in the soil.<br><br>CONCLUSION: The application of biosurfactants as a potent electrolyte for the remediation of hazardous pollutants is an integrated process. Overall, the results of this study suggest that biosurfactants can serve as an economic and efficient electrolyte in the EK process to remove Cr from polluted soil.},
}
@article {pmid39380672,
year = {2024},
author = {Yumnam, H and Hazarika, P and Sharma, I},
title = {Metagenomic insights into traditional fermentation of rice-based beverages among ethnic tribes in southern Assam, Northeast India.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1410098},
pmid = {39380672},
issn = {1664-302X},
abstract = {INTRODUCTION: Traditional fermented foods have long been recognized for their numerous health benefits along with their potential to aid in the treatment of gastrointestinal disorders. These fermented foods have been shown to promote gut health and contribute to a longer, healthier life.<br><br>METHODS: The high-throughput sequencing using the Illumina MiSeq platform was employed to investigate the microbiome communities of rice-based fermented beverages consumed by ethnic tribes in Southern Assam, namely Zeme Naga, Dimasa Kachari, Hmar, Karbi and Tea tribes.<br><br>RESULTS: The fermented rice-based beverages were highly predominated by Firmicutes, Bacteroides, Proteobacteria, and Actinobacteria exhibiting the highest relative abundance across all tribes. At genus level, significant abundance of pediococcus, lactobacillus, bacillus, leuconostoc, acetobacter, staphylococcus, delftia, erwinia, klebsiella and chrysebacterium were found amongst these ethnic tribes.<br><br>DISCUSSION: Understanding the fermented food microbiome will help to know the relationships between microbial communities and their effect on health of humans amongst the tribes. Furthermore, the use of these fermented products could provide enhanced health benefits to southern Assam region of India.},
}
@article {pmid39380403,
year = {2024},
author = {Pang, R and Wang, X and Zhang, L and Lei, L and Han, Z and Xie, B and Su, Y},
title = {Genome-Centric Metagenomics Insights into the Plastisphere-Driven Natural Degradation Characteristics and Mechanism of Biodegradable Plastics in Aquatic Environments.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c04965},
pmid = {39380403},
issn = {1520-5851},
abstract = {Biodegradable plastics (BPs) are pervasively available as alternatives to traditional plastics, but their natural degradation characteristics and microbial-driven degradation mechanisms are poorly understood, especially in aquatic environments, the primary sink of plastic debris. Herein, the three-month dynamic degradation process of BPs (the copolymer of poly(butylene adipate-co-terephthalate) and polylactic acid (PLA) (PBAT/PLA) and single PLA) in a natural aquatic environment was investigated, with nonbiodegradable plastics polyvinyl chloride, polypropylene, and polystyrene as controls. PBAT/PLA showed the weight loss of 47.4% at 50 days and severe fragmentation within two months, but no significant decay for other plastics. The significant increase in the specific surface area and roughness and the weakening of hydrophobicity within the first month promoted microbial attachment to the PBAT/PLA surface. Then, a complete microbial succession occurred, including biofilm formation, maturation, and dispersion. Metagenomic analysis indicated that plastispheres selectively enriched degraders. Based on the functional genes involved in BPs degradation, a total of 16 high-quality metagenome-assembled genomes of degraders (mainly Burkholderiaceae) were recovered from the PBAT/PLA plastisphere. These microbes showed the greatest degrading potential at the biofilm maturation stage and executed the functions by PLA_depolymerase, polyesterase, hydrolase, and esterase. These findings will enhance understanding of BPs' environmental behavior and microbial roles on plastic degradation.},
}
@article {pmid39380016,
year = {2024},
author = {Ju, Y and Zhang, Z and Liu, M and Lin, S and Sun, Q and Song, Z and Liang, W and Tong, X and Jie, Z and Lu, H and Cai, K and Chen, P and Jin, X and Zhang, W and Xu, X and Yang, H and Wang, J and Hou, Y and Xiao, L and Jia, H and Zhang, T and Guo, R},
title = {Integrated large-scale metagenome assembly and multi-kingdom network analyses identify sex differences in the human nasal microbiome.},
journal = {Genome biology},
volume = {25},
number = {1},
pages = {257},
pmid = {39380016},
issn = {1474-760X},
mesh = {Humans ; Male ; Female ; *Metagenome ; *Microbiota ; Adult ; Nose/microbiology ; Sex Characteristics ; Young Adult ; Bacteria/genetics/classification ; Sex Factors ; Metagenomics/methods ; },
abstract = {BACKGROUND: Respiratory diseases impose an immense health burden worldwide. Epidemiological studies have revealed extensive disparities in the incidence and severity of respiratory tract infections between men and women. It has been hypothesized that there might also be a nasal microbiome axis contributing to the observed sex disparities.<br><br>RESULTS: Here, we study the nasal microbiome of healthy young adults in the largest cohort to date with 1593 individuals, using shotgun metagenomic sequencing. We compile the most comprehensive reference catalog for the nasal bacterial community containing 4197 metagenome-assembled genomes and integrate the mycobiome, to provide a valuable resource and a more holistic perspective for the understudied human nasal microbiome. We systematically evaluate sex differences and reveal extensive sex-specific features in both taxonomic and functional levels in the nasal microbiome. Through network analyses, we capture markedly higher ecological stability and antagonistic potentials in the female nasal microbiome compared to the male's. The analysis of the keystone bacteria reveals that the sex-dependent evolutionary characteristics might have contributed to these differences.<br><br>CONCLUSIONS: In summary, we construct the most comprehensive catalog of metagenome-assembled-genomes for the nasal bacterial community to provide a valuable resource for the understudied human nasal microbiome. On top of that, comparative analysis in relative abundance and microbial co-occurrence networks identify extensive sex differences in the respiratory tract community, which may help to further our understanding of the observed sex disparities in the respiratory diseases.},
}
@article {pmid39086104,
year = {2024},
author = {Macher, JN and Martínez, A and Çakir, S and Cholley, PE and Christoforou, E and Curini Galletti, M and van Galen, L and García-Cobo, M and Jondelius, U and de Jong, D and Leasi, F and Lemke, M and Rubio Lopez, I and Sánchez, N and Sørensen, MV and Todaro, MA and Renema, W and Fontaneto, D},
title = {Enhancing metabarcoding efficiency and ecological insights through integrated taxonomy and DNA reference barcoding: A case study on beach meiofauna.},
journal = {Molecular ecology resources},
volume = {24},
number = {7},
pages = {e13997},
doi = {10.1111/1755-0998.13997},
pmid = {39086104},
issn = {1755-0998},
support = {T0206/37197/2021/kg//Stemmler Foundation/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; Animals ; *Electron Transport Complex IV/genetics ; Netherlands ; Biodiversity ; North Sea ; Invertebrates/genetics/classification ; Bathing Beaches ; Ecosystem ; Metagenomics/methods ; },
abstract = {Molecular techniques like metabarcoding, while promising for exploring diversity of communities, are often impeded by the lack of reference DNA sequences available for taxonomic annotation. Our study explores the benefits of combining targeted DNA barcoding and morphological taxonomy to improve metabarcoding efficiency, using beach meiofauna as a case study. Beaches are globally important ecosystems and are inhabited by meiofauna, microscopic animals living in the interstitial space between the sand grains, which play a key role in coastal biodiversity and ecosystem dynamics. However, research on meiofauna faces challenges due to limited taxonomic expertise and sparse sampling. We generated 775 new cytochrome c oxidase I DNA barcodes from meiofauna specimens collected along the Netherlands' west coast and combined them with the NCBI GenBank database. We analysed alpha and beta diversity in 561 metabarcoding samples from 24 North Sea beaches, a region extensively studied for meiofauna, using both the enriched reference database and the NCBI database without the additional reference barcodes. Our results show a 2.5-fold increase in sequence annotation and a doubling of species-level Operational Taxonomic Units (OTUs) identification when annotating the metabarcoding data with the enhanced database. Additionally, our analyses revealed a bell-shaped curve of OTU richness across the intertidal zone, aligning more closely with morphological analysis patterns, and more defined community dissimilarity patterns between supralittoral and intertidal sites. Our research highlights the importance of expanding molecular reference databases and combining morphological taxonomy with molecular techniques for biodiversity assessments, ultimately improving our understanding of coastal ecosystems.},
}
@article {pmid39379947,
year = {2024},
author = {Ariaeenejad, S and Zeinalabedini, M and Sadeghi, A and Gharaghani, S and Mardi, M},
title = {Enhancing nutritional and potential antimicrobial properties of poultry feed through encapsulation of metagenome-derived multi-enzymes.},
journal = {BMC biotechnology},
volume = {24},
number = {1},
pages = {76},
pmid = {39379947},
issn = {1472-6750},
abstract = {BACKGROUND: The encapsulation of metagenome-derived multi-enzymes presents a novel approach to improving poultry feed by enhancing nutrient availability and reducing anti-nutritional factors. By integrating and encapsulated enzymes such as carbohydrate-hydrolyzing enzymes, protease, lipase, and laccase into feed formulations, this method not only improves feed digestibility but also potentially contributes to animal health and productivity through antimicrobial properties.<br><br>RESULTS: This study investigates the encapsulation of metagenome-derived enzymes, including carbohydrate-hydrolyzing enzymes, protease, lipase, and laccase, using Arabic and Guar gums as encapsulating agents. The encapsulated multi-enzymes exhibited significant antimicrobial activity, achieving a 92.54% inhibition rate against Escherichia coli at a concentration of 6 U/mL. Fluorescence tracking with FITC-labeled enzymes confirmed efficient encapsulation and distribution, while physical characterization, including moisture content and solubility assessments, along with Atomic Force Microscopy (AFM) imaging, validated successful encapsulation. The encapsulated enzymes also effectively hydrolyzed poultry feed, leading to an increase in phenolic content and antioxidant activity, as confirmed by 2,2'-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid (ABTS) and 2,2-diphenyl-1-picrylhydrazyl (DPPH) assays.<br><br>CONCLUSIONS: The encapsulated multi-enzymes improved the overall feed quality by increasing reducing sugars and enhancing physical properties such as solubility and water-holding capacity. The encapsulated multi-enzymes improved the overall feed quality by increasing reducing sugars, antioxidant activity and enhancing physical properties such as solubility and water-holding capacity. Scanning Electron Microscopy (SEM) and Fourier-Transform Infrared Spectroscopy (FTIR) analyses confirmed the enzymatic breakdown of the feed structure. These results suggest that supplementing poultry feed with encapsulated multi-enzymes can enhance its physical, nutritional, and functional properties, leading to improved digestibility and overall feed quality.},
}
@article {pmid39379646,
year = {2024},
author = {Shaw, J and Yu, YW},
title = {Rapid species-level metagenome profiling and containment estimation with sylph.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {39379646},
issn = {1546-1696},
support = {RGPIN-2022-03074//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (Conseil de Recherches en Sciences Naturelles et en G&#xe9;nie du Canada)/ ; DGDND-2022-03074//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (Conseil de Recherches en Sciences Naturelles et en G&#xe9;nie du Canada)/ ; CGS-D//Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada (NSERC Canadian Network for Research and Innovation in Machining Technology)/ ; },
abstract = {Profiling metagenomes against databases allows for the detection and quantification of microorganisms, even at low abundances where assembly is not possible. We introduce sylph, a species-level metagenome profiler that estimates genome-to-metagenome containment average nucleotide identity (ANI) through zero-inflated Poisson k-mer statistics, enabling ANI-based taxa detection. On the Critical Assessment of Metagenome Interpretation II (CAMI2) Marine dataset, sylph was the most accurate profiling method of seven tested. For multisample profiling, sylph took >10-fold less central processing unit time compared to Kraken2 and used 30-fold less memory. Sylph's ANI estimates provided an orthogonal signal to abundance, allowing for an ANI-based metagenome-wide association study for Parkinson disease (PD) against 289,232 genomes while confirming known butyrate-PD associations at the strain level. Sylph took <1 min and 16 GB of random-access memory to profile metagenomes against 85,205 prokaryotic and 2,917,516 viral genomes, detecting 30-fold more viral sequences in the human gut compared to RefSeq. Sylph offers precise, efficient profiling with accurate containment ANI estimation even for low-coverage genomes.},
}
@article {pmid39379175,
year = {2024},
author = {Zheng, D and Wilén, BM and Öberg, O and Wik, T and Modin, O},
title = {"Metagenomics reveal the potential for geosmin and 2-methylisoborneol production across multiple bacterial phyla in recirculating aquaculture systems".},
journal = {Environmental microbiology},
volume = {26},
number = {10},
pages = {e16696},
doi = {10.1111/1462-2920.16696},
pmid = {39379175},
issn = {1462-2920},
support = {2020-02639//Svenska Forskningsr&#xe5;det Formas/ ; },
mesh = {*Metagenomics ; *Bacteria/genetics/classification/metabolism ; *Aquaculture ; *Naphthols/metabolism ; *Camphanes/metabolism ; Phylogeny ; Archaea/genetics/metabolism/classification ; Microbiota ; Metagenome ; },
abstract = {Geosmin and 2-methylisoborneol (MIB) are known to cause taste-and-odour problems in recirculating aquaculture systems (RAS). Both geosmin and MIB are microbial metabolites belonging to terpenoids. Precursors for terpenoids are biosynthesized via the methylerythritol phosphate (MEP) and the mevalonate (MVA) pathways. We carried out a metagenomic analysis of 50 samples from five RAS to investigate terpenoid biosynthesis and metabolic potential for geosmin and MIB production in RAS microbiomes. A total of 1008 metagenome-assembled genomes (MAGs) representing 26 bacterial and three archaeal phyla were recovered. Although most archaea are thought to use the MVA pathway for terpenoid precursor biosynthesis, an Iainarchaeota archaeal MAG is shown to harbour a complete set of genes encoding the MEP pathway but lacking genes associated with the MVA pathway. In this study, a total of 16 MAGs affiliated with five bacterial phyla (Acidobacteriota, Actinobacteriota, Bacteroidota, Chloroflexota, and Myxococcota) were identified as possessing potential geosmin or MIB synthases. These putative taste and odour producers were diverse, many were taxonomically unidentified at the genus or species level, and their relative abundance differed between the investigated RAS farms. The metagenomic study of the RAS microbiomes revealed a previously unknown phylogenetic diversity of the potential to produce geosmin and MIB.},
}
@article {pmid39378970,
year = {2024},
author = {Zharikova, AA and Andrianova, NV and Silachev, DN and Nebogatikov, VO and Pevzner, IB and Makievskaya, CI and Zorova, LD and Maleev, GV and Baydakova, GV and Chistyakov, DV and Goriainov, SV and Sergeeva, MG and Burakova, IY and Gureev, AP and Popkov, VA and Ustyugov, AA and Plotnikov, EY},
title = {Analysis of the brain transcriptome, microbiome and metabolome in ketogenic diet and experimental stroke.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bbi.2024.10.004},
pmid = {39378970},
issn = {1090-2139},
abstract = {The ketogenic diet (KD) has been shown to be effective in treating various brain pathologies. In this study, we conducted detailed transcriptomic and metabolomic profiling of rat brains after KD and ischemic stroke in order to investigate the effects of KD and its underlying mechanisms. We evaluated the effect of a two-month KD on gene expression in intact brain tissue and after middle cerebral artery occlusion (MCAO). We analyzed the effects of KD on gut microbiome composition and blood metabolic profile as well as investigated the correlation between severity of neurological deficits and KD-induced changes. We found transcriptional reprogramming in the brain after stroke and KD treatment. The KD altered the expression of genes involved in the regulation of glucose and fatty acid metabolism, mitochondrial function, the immune response, Wnt-associated signaling, stem cell development, and neurotransmission, both in intact rats and after MCAO. The KD led to a significant change in the composition of gut microbiome and the levels of amino acids, acylcarnitines, polyunsaturated fatty acids, and oxylipins in the blood. However, the KD slightly worsened the neurological functions after MCAO, so that the therapeutic effect of the diet remained unproven.},
}
@article {pmid39378879,
year = {2024},
author = {Wu, G and Xu, T and Zhao, N and Lam, YY and Ding, X and Wei, D and Fan, J and Shi, Y and Li, X and Li, M and Ji, S and Wang, X and Fu, H and Zhang, F and Shi, Y and Zhang, C and Peng, Y and Zhao, L},
title = {A core microbiome signature as an indicator of health.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2024.09.019},
pmid = {39378879},
issn = {1097-4172},
abstract = {The gut microbiota is crucial for human health, functioning as a complex adaptive system akin to a vital organ. To identify core health-relevant gut microbes, we followed the systems biology tenet that stable relationships signify core components. By analyzing metagenomic datasets from a high-fiber dietary intervention in type 2 diabetes and 26 case-control studies across 15 diseases, we identified a set of stably correlated genome pairs within co-abundance networks perturbed by dietary interventions and diseases. These genomes formed a "two competing guilds" (TCGs) model, with one guild specialized in fiber fermentation and butyrate production and the other characterized by virulence and antibiotic resistance. Our random forest models successfully distinguished cases from controls across multiple diseases and predicted immunotherapy outcomes through the use of these genomes. Our guild-based approach, which is genome specific, database independent, and interaction focused, identifies a core microbiome signature that serves as a holistic health indicator and a potential common target for health enhancement.},
}
@article {pmid39378756,
year = {2024},
author = {Wang, X and Chen, L and Yang, G and Cai, Y and Yu, G},
title = {Bacterial and fungal aerosols in poultry houses: PM2.5 metagenomics via single-molecule real-time sequencing.},
journal = {Poultry science},
volume = {103},
number = {12},
pages = {104348},
doi = {10.1016/j.psj.2024.104348},
pmid = {39378756},
issn = {1525-3171},
abstract = {Microbial aerosol contamination is a common problem in poultry farms, posing potential health risks to poultry and their caretakers. Exploring the distribution and diversity of the microbial community in poultry farm aerosols is crucial for effective mitigation strategies. The composition of bacterial and fungal aerosols is poorly understood, particularly the prevalence of potential pathogenic microorganisms in fine particulate matter (PM2.5) in various types of poultry houses. In this study, 27 PM2.5 samples were collected from 5 chicken houses and 4 duck houses in Shandong Province, China. Species-level diversity of bacterial and fungal components in PM2.5 samples was determined using advanced single-molecule real-time sequencing (SMRT) technology, based on the 16S and internal transcribed spacer 1 (ITS) ribosomal genes. Microbial diversity and community composition varied significantly across the different poultry house. Notably, duck houses had higher concentrations (p < 0.01) of PM2.5 (92.8-143.1 μg/m[3]) than chicken houses (42.0-56.4 μg/m[3]). Furthermore, microbial variation in PM2.5 samples was associated with the type of poultry facility. The predominant pathogenic microorganisms included Aspergillus sydowii, Penicillium sp., Aspergillus insolitus, Cladosporium sp., Aspergillus sp., Aspergillus pseudoglaucus, Cladosporium sp. C4092-2-PD1, and Colletotrichum sp., all of which were classified as second category of pathogens. Aspergillus sydowii and Penicillium sp. were the dominant species in chicken houses, while Cladosporium sp., Aspergillus sp., and Aspergillus pseudoglaucus were the dominant species identified in duck houses. To our knowledge, this study is the first to investigate bacterial and fungal diversity in PM2.5 samples collected from various types of poultry houses. These findings advance our understanding of poultry environmental microbiology and have important implications for safeguarding the health of both poultry and their caretakers.},
}
@article {pmid39378747,
year = {2024},
author = {Yang, G and Luo, Y and Bian, Y and Chen, X and Chen, L and Huang, X},
title = {Electro-mediated cathodic oxygen drives respiration chain electron transfer of electroactive bacteria to enhance refractory organic biological oxidation.},
journal = {Water research},
volume = {268},
number = {Pt A},
pages = {122585},
doi = {10.1016/j.watres.2024.122585},
pmid = {39378747},
issn = {1879-2448},
abstract = {In electro-mediated biological system (EMBS), biological anode and cathode components were incorporated into an anaerobic bioreactor, providing a small amount of oxygen to the cathode as an electron acceptor. Oxygen diffusion also impacts the anode's anaerobic ecological environment. This study unraveled how oxygen influences the metabolism and electron transport chain during the biological oxidation of refractory organics. Under the influence of electromotive force, the straight-chain model pollutant N,N-dimethylformamide (DMF) showed rapid degradation and better ammonification, with maximum rates reaching 0.53 h[-1] and 26.6 %, respectively. Elevated electromotive force promoted the enrichment of functional electroactive bacteria on the anode and enhanced the availability of electron storage sites, thereby facilitating electron transfer at the anode-biofilm interface. Conversely, the anodic micro-aerobic environment disrupted the anaerobic microbial community structure, and the competitive interactions among fermentative bacteria and electroactive bacteria inhibited DMF degradation. Metagenomic analysis confirmed that cathodic oxygen up-regulated the pyruvate metabolism and the tricarboxylic acid (TCA) cycle to generate NADH and synthesize ATP. The electromotive force induced by cathodic oxygen accelerated the electron transfer in respiratory chains of electroactive bacteria, driving the oxidation of NADH and enhancing the degradation of organics. This study improves our understanding of the regulatory mechanisms governing metabolic pathways under the influence of cathodic oxygen. It offers potential for developing more efficient EMBS in industrial wastewater pretreatment, ensuring that oxygen is prevented from diffusing to the anode during micro-aeration at the cathode.},
}
@article {pmid39378744,
year = {2024},
author = {Zhu, T and Li, S and Tao, C and Chen, W and Chen, M and Zong, Z and Wang, Y and Li, Y and Yan, B},
title = {Understanding the mechanism of microplastic-associated antibiotic resistance genes in aquatic ecosystems: Insights from metagenomic analyses and machine learning.},
journal = {Water research},
volume = {268},
number = {Pt A},
pages = {122570},
doi = {10.1016/j.watres.2024.122570},
pmid = {39378744},
issn = {1879-2448},
abstract = {The pervasive presence of microplastics (MPs) in aquatic systems facilitates the transmission of antibiotic resistance genes (ARGs), thereby posing risks to ecosystems and human well-being. However, owing to variations in environmental backgrounds and the limited scope of research subjects, studies on ARGs in MPs lack unified conclusions, particularly regarding whether different types of MPs selectively promote ARG enrichment. Analysing large-scale datasets can better encompass broad spatiotemporal scales and diverse samples, facilitating a more extensive exploration of the complex ecological relationships between MPs and ARGs. The present study integrated existing metagenomic datasets to conduct a comprehensive risk assessment and comparative analysis of resistance groups across various MPs. In addition, we endeavoured to elucidate potential associations between ARGs and bacterial taxa, as well as MP structural features, using machine learning (ML) methods. The findings of our research highlight the pivotal role of MP type in shaping plastispheres, accounting for 9.56 % of the biotic variation (Adonis index) and explaining 18.59 % of the ARG variance. Compared to conventional MPs, biodegradable MPs, such as polyhydroxyalkanoates (PHA) and polylactic acid (PLA), exhibit lower species uniformity and diversity but pose a higher risk of ARG occurrence. These ML approaches effectively forecasted ARG abundance by using the bacterial taxa and molecular structure descriptors (MDs) of MPs (average R[2]tra = 0.882, R[2]test = 0.759). Feature analysis showed that MDs associated with lipophilicity, solubility, toxicity, and surface potential significantly influenced the relative abundance of ARGs in the plastispheres. The interpretable multiple linear regression (MLR) model, particularly notable, elucidated a linear relationship between bacterial genera and ARGs, offering promise for identifying potential ARG hosts. This study offers novel insights into ARG dynamics and ecological risks within aquatic plastispheres, highlighting the importance of comprehensive MP monitoring initiatives.},
}
@article {pmid39378692,
year = {2024},
author = {Lappan, R and Chown, SL and French, M and Perlaza-Jiménez, L and Macesic, N and Davis, M and Brown, R and Cheng, A and Clasen, T and Conlan, L and Goddard, F and Henry, R and Knight, DR and Li, F and Luby, S and Lyras, D and Ni, G and Rice, SA and Short, F and Song, J and Whittaker, A and Leder, K and Lithgow, T and Greening, C},
title = {Towards integrated cross-sectoral surveillance of pathogens and antimicrobial resistance: Needs, approaches, and considerations for linking surveillance to action.},
journal = {Environment international},
volume = {192},
number = {},
pages = {109046},
doi = {10.1016/j.envint.2024.109046},
pmid = {39378692},
issn = {1873-6750},
abstract = {Pathogenic and antimicrobial-resistant (AMR) microorganisms are continually transmitted between human, animal, and environmental reservoirs, contributing to the high burden of infectious disease and driving the growing global AMR crisis. The sheer diversity of pathogens, AMR mechanisms, and transmission pathways connecting these reservoirs create the need for comprehensive cross-sectoral surveillance to effectively monitor risks. Current approaches are often siloed by discipline and sector, focusing independently on parts of the whole. Here we advocate that integrated surveillance approaches, developed through transdisciplinary cross-sector collaboration, are key to addressing the dual crises of infectious diseases and AMR. We first review the areas of need, challenges, and benefits of cross-sectoral surveillance, then summarise and evaluate the major detection methods already available to achieve this (culture, quantitative PCR, and metagenomic sequencing). Finally, we outline how cross-sectoral surveillance initiatives can be fostered at multiple scales of action, and present key considerations for implementation and the development of effective systems to manage and integrate this information for the benefit of multiple sectors. While methods and technologies are increasingly available and affordable for comprehensive pathogen and AMR surveillance across different reservoirs, it is imperative that systems are strengthened to effectively manage and integrate this information.},
}
@article {pmid39378072,
year = {2024},
author = {Koohi-Moghadam, M and Watt, RM and Leung, WK},
title = {Multi-site analysis of biosynthetic gene clusters from the periodontitis oral microbiome.},
journal = {Journal of medical microbiology},
volume = {73},
number = {10},
pages = {},
doi = {10.1099/jmm.0.001898},
pmid = {39378072},
issn = {1473-5644},
mesh = {Humans ; *Periodontitis/microbiology ; *Multigene Family ; *Mouth/microbiology ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation &amp; purification/metabolism ; Pilot Projects ; Metagenomics/methods ; Saliva/microbiology ; Adult ; Male ; Biosynthetic Pathways/genetics ; Female ; Middle Aged ; High-Throughput Nucleotide Sequencing ; Metagenome ; },
abstract = {Background. Bacteria significantly influence human health and disease, with bacterial biosynthetic gene clusters (BGCs) being crucial in the microbiome-host and microbe-microbe interactions.Gap statement. Despite extensive research into BGCs within the human gut microbiome, their roles in the oral microbiome are less understood.Aim. This pilot study utilizes high-throughput shotgun metagenomic sequencing to examine the oral microbiota in different niches, particularly focusing on the association of BGCs with periodontitis.Methodology. We analysed saliva, subgingival plaque and supragingival plaque samples from periodontitis patients (n=23) and controls (n=16). DNA was extracted from these samples using standardized protocols. The high-throughput shotgun metagenomic sequencing was then performed to obtain comprehensive genetic information from the microbial communities present in the samples.Results. Our study identified 10 742 BGCs, with certain clusters being niche-specific. Notably, aryl polyenes and bacteriocins were the most prevalent BGCs identified. We discovered several 'novel' BGCs that are widely represented across various bacterial phyla and identified BGCs that had different distributions between periodontitis and control subjects. Our systematic approach unveiled the previously unexplored biosynthetic pathways that may be key players in periodontitis.Conclusions. Our research expands the current metagenomic knowledge of the oral microbiota in both healthy and periodontally diseased states. These findings highlight the presence of novel biosynthetic pathways in the oral cavity and suggest a complex network of host-microbe and microbe-microbe interactions, potentially influencing periodontal disease. The BGCs identified in this study pave the way for future investigations into the role of small-molecule-mediated interactions within the human oral microbiota and their impact on periodontitis.},
}
@article {pmid39377977,
year = {2024},
author = {Tufail, MA and Schmitz, RA},
title = {Exploring the Probiotic Potential of Bacteroides spp. Within One Health Paradigm.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {39377977},
issn = {1867-1314},
support = {031B0846D//Bundesministerium f&#xfc;r Bildung und Forschung/ ; 031B0846D//Bundesministerium f&#xfc;r Bildung und Forschung/ ; },
abstract = {Probiotics are pivotal in maintaining or restoring the balance of human intestinal microbiota, a crucial factor in mitigating diseases and preserving the host's health. Exploration into Bacteroides spp. reveals substantial promise in their development as next-generation probiotics due to their profound interaction with host immune cells and capability to regulate the microbiome's metabolism by significantly impacting metabolite production. These beneficial bacteria exhibit potential in ameliorating various health issues such as intestinal disorders, cardiovascular diseases, behavioral disorders, and even cancer. Though it's important to note that a high percentage of them are as well opportunistic pathogens, posing risks under certain conditions. Studies highlight their role in modifying immune responses and improving health conditions by regulating lymphocytes, controlling metabolism, and preventing inflammation and cancer. The safety and efficacy of Bacteroides strains are currently under scrutiny by the European Commission for authorization in food processing, marking a significant step towards their commercialization. The recent advancements in bacterial isolation and sequencing methodologies, coupled with the integration of Metagenome-Assembled Genomes (MAGs) binning from metagenomics data, continue to unveil the potential of Bacteroides spp., aiding in the broader understanding and application of these novel probiotics in health and disease management.},
}
@article {pmid39377603,
year = {2024},
author = {Colberg, O and Hermes, GDA and Licht, TR and Wichmann, A and Baker, A and Laursen, MF and Wellejus, A},
title = {Development of an infant colon simulating in vitro model, I-TIM-2, to study the effects of modulation strategies on the infant gut microbiome composition and function.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0072424},
doi = {10.1128/spectrum.00724-24},
pmid = {39377603},
issn = {2165-0497},
abstract = {The early life stages are critical for the development of the gut microbiome. Variables such as antibiotics exposure, birth-mode via Cesarean section, and formula feeding are associated with disruptions in microbiome development and are related to adverse health effects later in life. Studying the effects of microbiome-modulating strategies in infants is challenged by appropriate ethical constraints. Therefore, we developed I-TIM-2, an infant in vitro colonic model based on the validated, computer-controlled, dynamic model of the colon, TIM-2. The system, consisting of four separate compartments, was inoculated with feces from four healthy, primarily breastfed infants, displaying distinctive microbiome profiles. For each infant's fecal sample, a 96-h experiment was performed, with two compartments receiving an infant diet adapted medium and two compartments additionally receiving five human milk oligosaccharides (HMOs) in physiological concentrations and proportions. Bacterial composition was determined by shotgun metagenomics and qPCR. Concentrations of short-chain fatty acids (SCFAs) and HMOs were determined by LC-MS. Microbial diversity and high amounts of inoculum-derived species were preserved in the model throughout each experiment. Microbiome composition and SCFA concentrations were consistent with published data from infants. HMOs strongly modulated the microbiome composition by stimulating relative proportions of Bifidobacterium. This affected the metabolic output and resulted in an increased production of acetic and formic acid, characteristic of bifidobacterial HMO metabolism. In conclusion, these data demonstrate the development of a valid model to study the dynamics and modulations of the infant gut microbiome and metabolome.IMPORTANCEThe infant gut microbiome is intricately linked to the health of its host. This is partly mediated through the bacterial production of metabolites that interact with the host cells. Human milk shapes the establishment of the infant gut microbiome as it contains human milk sugars that select for primarily bifidobacteria. The establishment can be disrupted by modern interventions such as formula feeding. This can alter the microbiome composition and metabolite production profile, which can affect the host. In this article, we set up an infant in vitro colonic model to study microbiome interactions and functions. In this model, we investigated the effects of human milk sugars and their promotion of bifidobacteria at the expense of other bacteria. The model is an ideal system to assess the effects of various modulating strategies on the infant gut microbiome and its interactions with its host.},
}
@article {pmid39377587,
year = {2024},
author = {McMillan, AS and Zhang, G and Dougherty, MK and McGill, SK and Gulati, AS and Baker, ES and Theriot, CM},
title = {Metagenomic, metabolomic, and lipidomic shifts associated with fecal microbiota transplantation for recurrent Clostridioides difficile infection.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0070624},
doi = {10.1128/msphere.00706-24},
pmid = {39377587},
issn = {2379-5042},
abstract = {Recurrent C. difficile infection (rCDI) is an urgent public health threat, for which the last resort and lifesaving treatment is a fecal microbiota transplant (FMT). However, the exact mechanisms that mediate a successful FMT are not well-understood. Here, we use longitudinal stool samples collected from patients undergoing FMT to evaluate intra-individual changes in the microbiome, metabolome, and lipidome after successful FMTs relative to their baselines pre-FMT. We show changes in the abundance of many lipids, specifically a decrease in acylcarnitines post-FMT, and a shift from conjugated bile acids pre-FMT to deconjugated secondary bile acids post-FMT. These changes correlate with a decrease in Enterobacteriaceae, which encode carnitine metabolism genes, and an increase in Lachnospiraceae, which encode bile acid altering genes such as bile salt hydrolases (BSHs) and the bile acid-inducible (bai) operon, post-FMT. We also show changes in gut microbe-encoded amino acid biosynthesis genes, of which Enterobacteriaceae was the primary contributor to amino acids C. difficile is auxotrophic for. Liquid chromatography, ion mobility spectrometry, and mass spectrometry (LC-IMS-MS) revealed a shift from microbial conjugation of primary bile acids pre-FMT to secondary bile acids post-FMT. Here, we define the structural and functional changes associated with a successful FMT and generate hypotheses that require further experimental validation. This information is meant to help guide the development of new microbiota-focused therapeutics to treat rCDI.IMPORTANCERecurrent C. difficile infection is an urgent public health threat, for which the last resort and lifesaving treatment is a fecal microbiota transplant. However, the exact mechanisms that mediate a successful FMT are not well-understood. Here, we show changes in the abundance of many lipids, specifically acylcarnitines and bile acids, in response to FMT. These changes correlate with Enterobacteriaceae pre-FMT, which encodes carnitine metabolism genes, and Lachnospiraceae post-FMT, which encodes bile salt hydrolases and baiA genes. There was also a shift from microbial conjugation of primary bile acids pre-FMT to secondary bile acids post-FMT. Here, we define the structural and functional changes associated with a successful FMT, which we hope will help aid in the development of new microbiota-focused therapeutics to treat rCDI.},
}
@article {pmid39377582,
year = {2024},
author = {Fukushima, K and Matsumoto, Y and Abe, Y and Hashimoto, K and Motooka, D and Kitada, S and Saito, H and Komukai, S and Fukui, E and Niitsu, T and Nabeshima, H and Nagahama, Y and Yamauchi, J and Nitta, T and Nii, T and Matsuki, T and Tsujino, K and Miki, K and Shintani, Y and Kumanogoh, A and Akira, S and Nakamura, S and Kida, H},
title = {Variability of macrolide-resistant profile in Mycobacterium avium complex pulmonary disease.},
journal = {Antimicrobial agents and chemotherapy},
volume = {},
number = {},
pages = {e0121324},
doi = {10.1128/aac.01213-24},
pmid = {39377582},
issn = {1098-6596},
abstract = {This single-center retrospective study aimed to analyze the variability of macrolide resistance (MR) in 68 patients with Mycobacterium avium complex pulmonary disease. Among 25 patients treated without macrolides, 13 (52%) reverted to macrolide-susceptible (MS) profiles. Only one (2%) of 43 patients who continued macrolide treatment showed this change. We compared 30 MR isolates with recent specimens. Among them, seven shifted to MS (five attributed to clonally related strains; two resulting from reinfection or polyclonal infection).},
}
@article {pmid39376708,
year = {2024},
author = {Villacís, JF and López-Rosero, A and Bustillos, JJ and Cadena, M and Yumiseva, CA and Grijalva, MJ and Villacís, AG},
title = {Bacterial microbiota from the gut of Rhodnius ecuadoriensis, a vector of Chagas disease in Ecuador's Central Coast and Southern Andes.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1464720},
pmid = {39376708},
issn = {1664-302X},
abstract = {INTRODUCTION: Chagas disease is a neglected tropical disease caused by the parasite Trypanosoma cruzi that is transmitted mainly by the feces of infected Triatomines. In Ecuador the main vector is Rhodnius ecuadoriensis which is distributed in several provinces of the country. More than 40% of these insects in the wild have T. cruzi as part of their intestinal microbiota. For this reason, the objective of this research was to characterize the intestinal bacterial microbiota of R. ecuadoriensis.<br><br>METHODS: The methodology used was based on the DNA extraction of the intestinal contents from the wild collected insects (adults and nymphs V), as well as the insects maintained at the insectary of the CISeAL. Finally, the samples were analyzed by metagenomics extensions based on the different selected criteria.<br><br>RESULTS: The intestinal microbiota of R. ecuadoriensis presented a marked divergence between laboratory-raised and wild collected insects. This difference was observed in all stages and was similar between insects from Loja and Manab&#xed;. A large loss of microbial symbionts was observed in laboratory-raised insects.<br><br>DISCUSSION: This study is a crucial first step in investigating microbiota interactions and advancing new methodologies.},
}
@article {pmid39376703,
year = {2024},
author = {Karnachuk, OV and Lukina, AP and Avakyan, MR and Kadnikov, VV and Begmatov, S and Beletsky, AV and Vlasova, KG and Novikov, AA and Shcherbakova, VA and Mardanov, AV and Ravin, NV},
title = {Novel thermophilic genera Geochorda gen. nov. and Carboxydochorda gen. nov. from the deep terrestrial subsurface reveal the ecophysiological diversity in the class Limnochordia.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1441865},
pmid = {39376703},
issn = {1664-302X},
abstract = {The class Limnochordia harbors a single cultivated member, the mesophilic Limnochorda pilosa, which was isolated from a meromictic lake. Despite numerous molecular signatures reported in various ecosystems, the ecophysiological versatility of this deeply branched lineage of Firmicutes (Bacillota) remains poorly understood. The objective of this study was to use targeted cultivation, based on metagenome-assembled genomes from a deep terrestrial aquifer in Western Siberia, to isolate two new thermophilic members of the class. These isolates, described as Geochorda subterranea gen. nov. sp. nov. and Carboxydochorda subterranea gen. nov. sp. nov. within the Geochordaceae fam. nov., were capable of both anaerobic and aerobic respiration using fumarate and O2, respectively, with simple sugars as electron donors. The cultivated Geochordaceae have demonstrated fermentative growth and degradation of various polymers, including starch, maltose, maltodextrin, xylan, and chitin. The carboxydotrophic C. subterranea sp. nov. exhibited autotrophic growth via the Calvin-Benson-Bassham cycle, using CO, H2, and formate as electron donors and O2 as an electron acceptor, adding metabolic flexibility to the bacterium in the nutrient-depleted "deep biosphere" and supporting the possibility of aerobic metabolism in the deep subsurface. The broad physiological potential deciphered from physiological experiments and comparative genomic data explains the widespread distribution of uncultivated members of the class Limnochordia in various ecosystems, where they can oxidize complex organic substrates through both aerobic and anaerobic respiration, as well as pursue a chemolithotrophic lifestyle through the oxidation of H2 or CO.},
}
@article {pmid39376702,
year = {2024},
author = {Wang, S and Li, Q and Ye, C and Ma, W and Sun, Y and Zhao, B and Zeng, W and Yue, Z and Li, L and Li, D},
title = {Effects of mulch films with different thicknesses on the microbial community of tobacco rhizosphere soil in Yunnan laterite.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1458470},
pmid = {39376702},
issn = {1664-302X},
abstract = {The mulch film (MF) management model of the agricultural field affects the physical and chemical properties of soil (PCPS) and the structure of the microorganism community; however, studies on the relationship between the rhizosphere microorganism community structure and the thickness of MF are still limited. To understand the interactions among the MF thickness, PCPS, and rhizosphere microorganism, a study was conducted by using an integrated metagenomic strategy, where tobacco rhizosphere soil was treated with four commonly representative and used thicknesses of MFs (0.004, 0.006, 0.008, and 0.010 mm) in Yunnan laterite. The results showed that agronomic traits such as the tobacco plant height (TPH), leaf number (LN), fresh leaf weight (FLW), and dry leaf weight (DLW) were significantly (p < 0.01) improved in the field mulched with the thickest film (0.010 mm) compared with the exposed field (CK), and there was a 6.81 and 5.54% increase in the FLW and TPH, separately. The correlation analyses revealed a significant positive correlation of the MF thickness with the soil water content (SWC), soil organic matter (SOM), total nitrogen (TN), available nitrogen (AN), total phosphorus (TP), and available phosphorus (AP; all p < 0.01), while the MF thickness was negatively correlated with the soil temperature (ST; p < 0.01). In addition, the community structure of the rhizosphere soil bacteria was significantly changed overall by the MF thickness, which also interfered with the function of the rhizosphere soil bacteria. The correlation analyses also showed that the abundance of Bradyrhizobium and Nitrospira was positively correlated with the MF thickness, while the abundance of Sphinsinomonas and Massilia was negatively correlated with it. This indicated that with the increase of the MF thickness, the ability of the rhizosphere soil to utilize N and remove harmful molecules was strengthened, while the capacity of the rhizosphere soil to degrade pollutants was greatly reduced. These findings provide additional insights into the potential risks of the application of different thicknesses of MFs, particularly concerning the PCPS and soil microbial communities.},
}
@article {pmid39376649,
year = {2024},
author = {Kang, Y and Zhang, X and Qin, C and Zheng, Y and Gai, W and Jia, X and Shao, B and Zhang, S and Jiang, H and Huang, X and Jia, J},
title = {Rapid diagnosis of Aspergillus flavus infection in acute very severe aplastic anemia with metagenomic next-generation sequencing: a case report and literature review.},
journal = {Frontiers in medicine},
volume = {11},
number = {},
pages = {1413964},
pmid = {39376649},
issn = {2296-858X},
abstract = {Infection remains the leading cause of mortality in severe aplastic anemia (SAA) patients, with invasive fungal infections being the great threat. Aspergillus fumigatus accounts for most of the reported fungal infection cases. Here, we present a case of A. flavus infection in a patient with acute very severe aplastic anemia (VSAA) despite persistently negative clinical fungal tests. The patient was admitted to the hospital due to pancytopenia presisting for over a month and intermittent fever for 10 days. Elevated inflammatory indicators and abnormal lung imaging suggested infection, prompting consideration of fungal involvement. Despite negative results from multiple blood, sputum fungal cultures and the serum (1,3)-β-D-glucan/galactomannan tests. Metagenomic next-generation sequencing (mNGS) on multiple blood samples, alongside clinical symptoms, confirmed A. flavus infection. Targeted antifungal treatment with liposomal amphotericin B and voriconazole significantly ameliorated pulmonary symptoms. Additionally, this study reviewed and compared the symptoms, diagnostic approaches, and treatments from prior Aspergillus infections in AA patients. It emphasizes critical role of early mNGS utilization in diagnosing and managing infectious diseases, offering insights for diagnosing and treating fungal infections in VSAA.},
}
@article {pmid39376581,
year = {2024},
author = {Du, Y and Qian, C and Li, X and Zheng, X and Huang, S and Yin, Z and Chen, T and Pan, L},
title = {Unveiling intraspecific diversity and evolutionary dynamics of the foodborne pathogen Bacillus paranthracis through high-quality pan-genome analysis.},
journal = {Current research in food science},
volume = {9},
number = {},
pages = {100867},
pmid = {39376581},
issn = {2665-9271},
abstract = {Understanding the evolutionary dynamics of foodborne pathogens throughout host-associated habitats is of utmost importance. Bacterial pan-genomes, as dynamic entities, are strongly influenced by ecological lifestyles. As a phenotypically diverse species in the Bacillus cereus group, Bacillus paranthracis is recognized as an emerging foodborne pathogen and a probiotic simultaneously. This poorly understood species is a suitable study model for adaptive pan-genome evolution. In this study, we determined the biogeographic distribution, abundance, genetic diversity, and genotypic profiles of key genetic elements of B. paranthracis. Metagenomic read recruitment analyses demonstrated that B. paranthracis members are globally distributed and abundant in host-associated habitats. A high-quality pan-genome of B. paranthracis was subsequently constructed to analyze the evolutionary dynamics involved in ecological adaptation comprehensively. The open pan-genome indicated a flexible gene repertoire with extensive genetic diversity. Significant divergences in the phylogenetic relationships, functional enrichment, and degree of selective pressure between the different components demonstrated different evolutionary dynamics between the core and accessory genomes driven by ecological forces. Purifying selection and gene loss are the main signatures of evolutionary dynamics in B. paranthracis pan-genome. The plasticity of the accessory genome is characterized by horizontal gene transfer (HGT), massive gene losses, and weak purifying or positive selection, which might contribute to niche-specific adaptation. In contrast, although the core genome dominantly undergoes purifying selection, its association with HGT and positively selected mutations indicates its potential role in ecological diversification. Furthermore, host fitness-related dynamics are characterized by the loss of secondary metabolite biosynthesis gene clusters (BGCs) and CAZyme-encoding genes and the acquisition of antimicrobial resistance (AMR) and virulence genes via HGT. This study offers a case study of pan-genome evolution to investigate the ecological adaptations reflected by biogeographical characteristics, thereby advancing the understanding of intraspecific diversity and evolutionary dynamics of foodborne pathogens.},
}
@article {pmid39376101,
year = {2024},
author = {Trujillo-Gómez, J and Navarro, CE and Atehortúa-Muñoz, S and Florez, ID},
title = {Acute infections of the central nervous system in children and adults: diagnosis and management.},
journal = {Minerva medica},
volume = {115},
number = {4},
pages = {476-502},
doi = {10.23736/S0026-4806.24.09097-9},
pmid = {39376101},
issn = {1827-1669},
mesh = {Humans ; Child ; *Central Nervous System Infections/diagnosis/therapy/drug therapy/microbiology ; Adult ; Acute Disease ; Risk Factors ; },
abstract = {Central nervous system infections are due to different microorganisms such as viruses, bacteria, mycobacteria, fungi, amoebas, and other parasites. The etiology depends on multiple risk factors, and it defines the infection location because some microorganisms prefer meninges, brain tissue, cerebellum, brain stem or spinal cord. The microorganisms induce diseases in the nervous system through direct invasion, neurotoxin production, and the triggered immune response. To determine the infection etiology, there are several diagnostic tests which may be conducted with cerebrospinal fluid, blood, respiratory and stool samples. These tests include but are not limited to direct microscopic examination of the sample, stains, cultures, antigenic tests, nucleic acid amplification tests, metagenomic next-generation sequencing, immunologic biomarker and neuroimaging, especially contrast-enhanced magnetic resonance imaging. The treatment may consist of specific antimicrobial treatment and supportive standard care. Since viruses have no specific antiviral treatment, antimicrobial treatment is mainly targeted at non-viral infections. This article will focus on diagnosis and treatment of acute acquired infections of the central nervous system beyond the neonatal period. The discussion defines the disease, provides the clinical presentation, explains the etiology and risk factors, and briefly mentions potential complications. This updated review aims to provide the reader with all the elements needed to adequately approach a patient with a central nervous system infection. Mycobacterium tuberculosis infection, Cryptococcus spp. infection and vaccines are not within the scope of this article.},
}
@article {pmid39375774,
year = {2024},
author = {Kosmopoulos, JC and Klier, KM and Langwig, MV and Tran, PQ and Anantharaman, K},
title = {Viromes vs. mixed community metagenomes: choice of method dictates interpretation of viral community ecology.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {195},
pmid = {39375774},
issn = {2049-2618},
mesh = {*Virome/genetics ; *Viruses/genetics/classification/isolation &amp; purification ; *Metagenomics/methods ; Humans ; *Metagenome ; *Genome, Viral/genetics ; Microbiota/genetics ; Soil Microbiology ; Fresh Water/virology/microbiology ; Gastrointestinal Microbiome/genetics ; },
abstract = {BACKGROUND: Viruses, the majority of which are uncultivated, are among the most abundant biological entities on Earth. From altering microbial physiology to driving community dynamics, viruses are fundamental members of microbiomes. While the number of studies leveraging viral metagenomics (viromics) for studying uncultivated viruses is growing, standards for viromics research are lacking. Viromics can utilize computational discovery of viruses from total metagenomes of all community members (hereafter metagenomes) or use physical separation of virus-specific fractions (hereafter viromes). However, differences in the recovery and interpretation of viruses from metagenomes and viromes obtained from the same samples remain understudied.<br><br>RESULTS: Here, we compare viral communities from paired viromes and metagenomes obtained from 60 diverse samples across human gut, soil, freshwater, and marine ecosystems. Overall, viral communities obtained from viromes had greater species richness and total viral genome abundances than those obtained from metagenomes, although there were some exceptions. Despite this, metagenomes still contained many viral genomes not detected in viromes. We also found notable differences in the predicted lytic state of viruses detected in viromes vs metagenomes at the time of sequencing. Other forms of variation observed include genome presence/absence, genome quality, and encoded protein content between viromes and metagenomes, but the magnitude of these differences varied by environment.<br><br>CONCLUSIONS: Overall, our results show that the choice of method can lead to differing interpretations of viral community ecology. We suggest that the choice of whether to target a metagenome or virome to study viral communities should be dependent on the environmental context and ecological questions being asked. However, our overall recommendation to researchers investigating viral ecology and evolution is to pair both approaches to maximize their respective benefits. Video Abstract.},
}
@article {pmid39375348,
year = {2024},
author = {Kang, X and Zhang, W and Li, Y and Luo, X and Schönhuth, A},
title = {HyLight: Strain aware assembly of low coverage metagenomes.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {8665},
pmid = {39375348},
issn = {2041-1723},
mesh = {*Metagenome/genetics ; *High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; Microbiota/genetics ; Sequence Analysis, DNA/methods ; Bacteria/genetics/classification ; Genome, Bacterial ; Software ; },
abstract = {Different strains of identical species can vary substantially in terms of their spectrum of biomedically relevant phenotypes. Reconstructing the genomes of microbial communities at the level of their strains poses significant challenges, because sequencing errors can obscure strain-specific variants. Next-generation sequencing (NGS) reads are too short to resolve complex genomic regions. Third-generation sequencing (TGS) reads, although longer, are prone to higher error rates or substantially more expensive. Limiting TGS coverage to reduce costs compromises the accuracy of the assemblies. This explains why prior approaches agree on losses in strain awareness, accuracy, tendentially excessive costs, or combinations thereof. We introduce HyLight, a metagenome assembly approach that addresses these challenges by implementing the complementary strengths of TGS and NGS data. HyLight employs strain-resolved overlap graphs (OG) to accurately reconstruct individual strains within microbial communities. Our experiments demonstrate that HyLight produces strain-aware and contiguous assemblies at minimal error content, while significantly reducing costs because utilizing low-coverage TGS data. HyLight achieves an average improvement of 19.05% in preserving strain identity and demonstrates near-complete strain awareness across diverse datasets. In summary, HyLight offers considerable advances in metagenome assembly, insofar as it delivers significantly enhanced strain awareness, contiguity, and accuracy without the typical compromises observed in existing approaches.},
}
@article {pmid39375020,
year = {2024},
author = {Garritano, AN and Zhang, Z and Jia, Y and Allen, MA and Hill, LJ and Kuzhiumparambil, U and Hinkley, C and Raina, JB and Peixoto, RS and Thomas, T},
title = {Simple Porifera holobiont reveals complex interactions between the host, an archaeon, a bacterium, and a phage.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae197},
pmid = {39375020},
issn = {1751-7370},
abstract = {The basal metazoan phylum, Porifera (sponges), is increasingly used as a model to investigate ecological and evolutionary features of microbe-animal symbioses. However, sponges often host complex microbiomes, which has hampered our understanding of their interactions with their microbial symbionts. Here, we describe the discovery and characterisation of the simplest sponge holobiont reported to date, consisting of the deep-sea glass sponge Aphrocalistes beatrix and two newly described microbial symbionts: an autotrophic ammonia-oxidising archaeon and a bacterial heterotroph. Omics analyses and metabolic modelling revealed the dependency of the ammonia-oxidising archaea on sponge-derived ammonia to drive primary production, which in turn supports the bacterium's growth by providing the dicarboxylate fumarate. Furthermore, virus-mediated archaeal lysis appears crucial to overcome the bacterium's vitamin B12 auxotrophy. These findings reveal that the exchange of vitamin B12 and dicarboxylate may be evolutionarily conserved features of symbiosis as they can also be found in interactions between free-living marine bacteria, and between microbes and plants or diatoms.},
}
@article {pmid39375018,
year = {2024},
author = {Yang, Q and Zhong, Y and Feng, SW and Wen, P and Wang, H and Wu, J and Yang, S and Liang, JL and Li, D and Yang, Q and Tam, NFY and Peng, P},
title = {Temporal enrichment of comammox Nitrospira and Ca. Nitrosocosmicus in a coastal plastisphere.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae186},
pmid = {39375018},
issn = {1751-7370},
abstract = {Plastic marine debris is known to harbor a unique microbiome (termed the "plastisphere") that can be important in marine biogeochemical cycles. However, the temporal dynamics in the plastisphere and their implications for marine biogeochemistry remain poorly understood. Here, we characterized the temporal dynamics of nitrifying communities in the plastisphere of plastic ropes exposed to a mangrove intertidal zone. The 39-month colonization experiment revealed that the relative abundances of Nitrospira and Candidatus Nitrosocosmicus representatives increased over time according to 16S rRNA gene amplicon sequencing analysis. The relative abundances of amoA genes in metagenomes implied that comammox Nitrospira were the dominant ammonia oxidizers in the plastisphere, and their dominance increased over time. The relative abundances of two metagenome-assembled genomes of comammox Nitrospira also increased with time and positively correlated with extracellular polymeric substances content of the plastisphere but negatively correlated with NH4+ concentration in seawater, indicating the long-term succession of these two parameters significantly influenced the ammonia-oxidizing community in the coastal plastisphere. At the end of the colonization experiment, the plastisphere exhibited high nitrification activity, leading to the release of N2O (2.52 ng N2O N g-1) in a 3-day nitrification experiment. The predicted relative contribution of comammox Nitrospira to N2O production (17.9%) was higher than that of ammonia-oxidizing bacteria (4.8%) but lower than that of ammonia-oxidizing archaea (21.4%). These results provide evidence that from a long-term perspective, some coastal plastispheres will become dominated by comammox Nitrospira and thereby act as hotspots of ammonia oxidation and N2O production.},
}
@article {pmid39374795,
year = {2024},
author = {Behl, S and Kusuma, V and Cardoso, T and Hamed, A and Almheiri, G and Kazi, S and Shanmugam, B and Brudecki, G and Vaylombran, D and Quilez, J and Elamin, W},
title = {Whole genome sequencing approaches for taxonomic profiling and evaluation of wastewater quality.},
journal = {Journal of microbiological methods},
volume = {},
number = {},
pages = {107051},
doi = {10.1016/j.mimet.2024.107051},
pmid = {39374795},
issn = {1872-8359},
abstract = {Tracking metagenomic abundance in wastewater is undoubtedly a powerful tool to detect emerging variants and improve community health. However, there are a few factors that limit environmental water-based genomic monitoring: sampling variability, incomplete coverage, genetic fragmentation, degradation, data analysis and interpretation. The decreasing costs of high-throughput sequencing and high-end supercomputers have increased the use and accuracy of genomic data for microbial detection and monitoring in wastewater samples within any given region. To better understand the microbial dynamics and to determine the target sequencing throughput required to establish taxa that may pose as bio-indicators of an epidemiological outbreak, wastewater samples were collected from distinct locations within the Emirate of Abu Dhabi, United Arab Emirates using appropriate sampling methods. A reference database of ~27,000 known species was developed and used for further analysis. The results showed that 15 % of data in each sample matched any of ~27,000 known bacterial, viral, fungal, or protozoan species. Despite the high fraction of unclassified data (85 %), more than 2000 species from >800 genera across >30 phyla were detected in each sample. Both 5 Gb and 10 Gb of sequenced data detected the top ~2000 species with highest abundance. Doubling the target sequencing throughput (i.e., 10 Gb vs 5 Gb) detected ~500 additional low-abundance species per sample however it did not affect the overall sample composition or translate into higher per-sample species diversity captured. There was a marginal increase in the number of species detected in each sample beyond 0.20 Gb of classified data. Overall, the results indicate that sequencing to a 3 Gb throughput detects nearly 95 % of all species in the samples.},
}
@article {pmid39374754,
year = {2024},
author = {Zhi, Q and Zheng, B and Teng, K and Xiao, Y and Zhou, X and Tang, Q and Li, J and Yin, H and Meng, D and Liu, T},
title = {Metagenomic approach reveals the role of bioagents in the environmental dissemination risk of rhizosphere soil antibiotic resistance genes pollution.},
journal = {Environmental research},
volume = {},
number = {},
pages = {120090},
doi = {10.1016/j.envres.2024.120090},
pmid = {39374754},
issn = {1096-0953},
abstract = {Antibiotic resistance genes (ARGs) have been identified as emerging contaminants, raising concerns around the world. As environmentally friendly bioagents (BA), plant growth-promoting rhizobacteria (PGPR) have been used in agricultural systems. The introduction of BA will lead to the turnover of the microbial communities structure. Nevertheless, it is still unclear how the colonization of the invaded microorganisms could affects the rhizosphere resistome. Consequently, 190 ARGs and 25 integrative and conjugative elements (ICEs) were annotated using the metagenomic approach in 18 samples from the Solanaceae crop rhizosphere soil under BA and conventional treatment (CK) groups. Our study found that, after 90 days of treatment, ARG abundance was lower in the CK group than in the BA group. The results showed that aminoglycoside antibiotic resistance (OprZ), phenicol antibiotic resistance (OprN), aminoglycoside antibiotic resistance (ceoA/B), aminocoumarin antibiotic resistance (mdtB) and phenicol antibiotic resistance (MexW) syntenic with ICEs. Moreover, in 11 sequences, OprN (phenicol antibiotic resistance) was observed to have synteny with ICEPaeLESB58-1, indicating that the ICEs could contribute to the spread of ARGs. Additionally, the binning result showed that the potential bacterial hosts of the ARGs were beneficial bacteria which could promote the nutrition cycle, such as Haliangium, Nitrospira, Sideroxydans, Burkholderia, etc, suggesting that bacterial hosts have a great influence on ARG profiles. According to the findings, considering the dissemination of ARGs, BA should be applied with caution, especially the use of beneficial bacteria in BA. In a nutshell, this study offers valuable insights into ARGs pollution control from the perspective of the development and application of BA, to make effective strategies for blocking pollution risk migration in the ecological environment.},
}
@article {pmid39374753,
year = {2024},
author = {Pushkareva, E and Hejduková, E and Elster, J and Becker, B},
title = {Microbial response to seasonal variation in Arctic biocrusts with a focus on fungi and cyanobacteria.},
journal = {Environmental research},
volume = {},
number = {},
pages = {120110},
doi = {10.1016/j.envres.2024.120110},
pmid = {39374753},
issn = {1096-0953},
abstract = {Biocrusts are crucial components of Arctic ecosystems, playing significant roles in carbon and nitrogen cycling, especially in regions where plant growth is limited. However, the microbial communities within Arctic biocrusts and their strategies for surviving the harsh conditions remain poorly understood. In this study, the microbial profiles of Arctic biocrusts across different seasons (summer, autumn, and winter) were investigated in order to elucidate their survival strategies in extreme conditions. Metagenomic and metatranscriptomic analyses revealed significant differences in microbial community composition among the sites located in different elevations. The bacterial communities were dominated by Actinobacteria and Proteobacteria, while the fungal communities were mainly represented by Ascomycota and Basidiomycota, with lichenized and saprotrophic traits prevailing. Cyanobacteria were primarily composed of heterocystous cyanobacteria. Furthermore, the study identified molecular mechanisms underlying cold adaptation, including the expression of heat shock proteins and cold-inducible RNA helicases in cyanobacteria and fungi. Overall, the microbial communities appear to be permanently well adapted to the extreme environment.},
}
@article {pmid39374327,
year = {2024},
author = {Liu, Y and Rohwerder, T and Bonatelli, ML and von Postel, T and Kleinsteuber, S and Adrian, L and Ding, C},
title = {A Novel Sulfatase for Acesulfame Degradation in Wastewater Treatment Plants as Evidenced from Shinella Strains.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c02283},
pmid = {39374327},
issn = {1520-5851},
abstract = {The artificial sweetener acesulfame is a persistent pollutant in wastewater worldwide. So far, only a few bacterial isolates were recently found to degrade acesulfame efficiently. In Bosea and Chelatococcus strains, a Mn[2+]-dependent metallo-β-lactamase-type sulfatase and an amidase signature family enzyme catalyze acesulfame hydrolysis via acetoacetamide-N-sulfonate to acetoacetate. Here, we describe a new acesulfame sulfatase in Shinella strains isolated from wastewater treatment plants in Germany. Their genomes do not encode the Mn[2+]-dependent sulfatase. Instead, a formylglycine-dependent sulfatase gene was found, together with the acetoacetamide-N-sulfonate amidase gene on a plasmid shared by all known acesulfame-degrading Shinella strains. Heterologous expression, proteomics, and size exclusion chromatography corroborated the physiological function of the Shinella sulfatase in acesulfame hydrolysis. Since both acesulfame sulfatase types are absent in other bacterial genomes or metagenome-assembled genomes, we surveyed 73 tera base pairs of wastewater-associated metagenome raw data sets. Bosea/Chelatococcus sulfatase gene signatures were regularly found from 2013, particularly in North America, Europe, and East Asia, whereas Shinella sulfatase gene signatures were first detected in 2020. Moreover, signatures for the Shinella sulfatase and amidase genes co-occur only in six data sets from China, Finland, and Mexico, suggesting that the Shinella genes were enriched or introduced quite recently in wastewater treatment facilities.},
}
@article {pmid39373542,
year = {2024},
author = {Rolland, C and Wittmann, J and Reimer, LC and Sardà Carbasse, J and Schober, I and Dudek, CA and Ebeling, C and Koblitz, J and Bunk, B and Overmann, J},
title = {PhageDive: the comprehensive strain database of prokaryotic viral diversity.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkae878},
pmid = {39373542},
issn = {1362-4962},
support = {SPP 2330//Deutsche Forschungsgemeinschaft/ ; },
abstract = {Prokaryotic viruses represent the most diverse and abundant biological entities on Earth. So far, data on bacteriophages are not standardized, not readily available for comparative analyses and cannot be linked to the rapidly growing (meta)genomic data. We developed PhageDive (https://phagedive.dsmz.de), a comprehensive database for prokaryotic viruses gathering all existing data dispersed across multiple sources, like scientific publications, specialized databases or internal files of culture collections. PhageDive allows to link own research data to the existing information through an easy and central access, providing fields for various experimental data (host range, genomic data, etc.) and available metadata (e.g. geographical origin, isolation source). An important feature is the link between experimental data, the culture collection number and the repository of the corresponding physical bioresource. To date, PhageDive covers 1167 phages from three different world-renowned public collections (DSMZ, Félix d'Hérelle Reference Center for Bacterial Viruses and NCTC) and features an advanced search function using all data fields from the sections like taxonomy or morphology by controlled vocabulary and ontologies. PhageDive is fully interoperable with other resources including NCBI, the Viral Host Range database (VHRdb) of Institute Pasteur or the BacDive and MediaDive databases of DSMZ.},
}
@article {pmid39373498,
year = {2024},
author = {Ojeda, A and Akinsuyi, O and McKinley, KL and Xhumari, J and Triplett, EW and Neu, J and Roesch, LFW},
title = {Increased antibiotic resistance in preterm neonates under early antibiotic use.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0028624},
doi = {10.1128/msphere.00286-24},
pmid = {39373498},
issn = {2379-5042},
abstract = {UNLABELLED: The standard use of antibiotics in newborns to empirically treat early-onset sepsis can adversely affect the neonatal gut microbiome, with potential long-term health impacts. Research into the escalating issue of antimicrobial resistance in preterm infants and antibiotic practices in neonatal intensive care units is limited. A deeper understanding of the effects of early antibiotic intervention on antibiotic resistance in preterm infants is crucial. This retrospective study employed metagenomic sequencing to evaluate antibiotic resistance genes (ARGs) in the meconium and subsequent stool samples of preterm infants enrolled in the Routine Early Antibiotic Use in Symptomatic Preterm Neonates study. Microbial metagenomics was conducted using a subset of fecal samples from 30 preterm infants for taxonomic profiling and ARG identification. All preterm infants exhibited ARGs, with 175 unique ARGs identified, predominantly associated with beta-lactam, tetracycline, and aminoglycoside resistance. Notably, 23% of ARGs was found in preterm infants without direct or intrapartum antibiotic exposure. Post-natal antibiotic exposure increases beta-lactam/tetracycline resistance while altering mechanisms that aid bacteria in withstanding antibiotic pressure. Microbial profiling revealed 774 bacterial species, with antibiotic-naive infants showing higher alpha diversity (P = 0.005) in their microbiota and resistome compared with treated infants, suggesting a more complex ecosystem. High ARG prevalence in preterm infants was observed irrespective of direct antibiotic exposure and intensifies with age. Prolonged membrane ruptures and maternal antibiotic use during gestation and delivery are linked to alterations in the preterm infant resistome and microbiome, which are pivotal in shaping the ARG profiles in the neonatal gut.This study is registered with ClinicalTrials.gov as NCT02784821.<br><br>IMPORTANCE: A high burden of antibiotic resistance in preterm infants poses significant challenges to neonatal health. The presence of antibiotic resistance genes, along with alterations in signaling, energy production, and metabolic mechanisms, complicates treatment strategies for preterm infants, heightening the risk of ineffective therapy and exacerbating outcomes for these vulnerable neonates. Despite not receiving direct antibiotic treatment, preterm infants exhibit a concerning prevalence of antibiotic-resistant bacteria. This underscores the complex interplay of broader influences, including maternal antibiotic exposure during and beyond pregnancy and gestational complications like prolonged membrane ruptures. Urgent action, including cautious antibiotic practices and enhanced antenatal care, is imperative to protect neonatal health and counter the escalating threat of antimicrobial resistance in this vulnerable population.},
}
@article {pmid39373481,
year = {2024},
author = {Nesbø, CL and Yang, MI and Sharan, AA and Meyer, T and Edwards, EA},
title = {Metagenomes and metagenome assembled genomes from anaerobic digesters at three Canadian pulp and paper mills.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0056124},
doi = {10.1128/mra.00561-24},
pmid = {39373481},
issn = {2576-098X},
abstract = {We present a dataset of six metagenomes and 323 metagenome assembled genomes (MAGs) describing the microbial community of anaerobic digesters at three Canadian pulp and paper mills. Our objective was to assess the coding potential of the microbial community and obtain draft genomes of key organisms in the digesters.},
}
@article {pmid39372894,
year = {2024},
author = {Liu, KL and Xu, SJ and Chen, SW and Zhang, MJ and Ye, N and Li, J},
title = {Correlation Analysis of Characteristics of Intestinal Microbiota and Cytokine Levels in Patients with Obstructive Sleep Apnea-Hypopnea Syndrome.},
journal = {Nature and science of sleep},
volume = {16},
number = {},
pages = {1533-1544},
pmid = {39372894},
issn = {1179-1608},
abstract = {OBJECTIVE: The aim of this study was to analyze the relationship between the characteristics of the intestinal microbiota and cytokine levels in individuals with different degrees of obstructive sleep apnea-hypopnea syndrome (OSAHS) as well as to investigate intestinal microbiota imbalances in patients with OSAHS and the associated mechanisms.<br><br>METHODS: Based on their sleep apnea hypopnea index (AHI), a total of 37 adults were assigned to a control group, a mild OSAHS group, or a moderate-to-severe OSAHS group. Fecal samples were collected to characterize the intestinal microbiota using metagenomic next-generation sequencing (mNGS), while blood samples were collected to detect levels of interleukin-17a (IL-17a), interleukin-10 (IL-10), tumor necrosis factor-alpha (TNF-&#x3b1;), and interleukin-6 (IL-6) in each group.<br><br>RESULTS: 1. There was no significant difference in the Shannon index among the three groups (P > 0.05). The three groups showed significant difference in the relative abundance of Faecalibacterium prausnitzii and Bifidobacterium adolescentis (with F values of 3.955 and 7.24, respectively, P < 0.05), while showed no significant difference in the relative abundance of B. pseudocatenulatum, Bifidobacterium longum, Klebsiella pneumoniae, and Haemophilus parainfluenzae (P > 0.05). 2. The three groups showed significant difference in the expression of serum IL-17A and TNF-&#x3b1; levels (with F values of 18.119 and 10.691, respectively, P < 0.05), while showed no significant difference in the expression of IL-10, IL-6, and CRP levels (P > 0.05). 3. Multiple linear regression analysis revealed that the relative abundance of F. prausnitzii was correlated with changes in BMI and AHI (with &#x3b2; values of 2.585 and -0.157, respectively, P < 0.05), while the relative abundance of B. adolescentis was correlated with changes in IL-17a (with &#x3b2; value of -0.161, P < 0.05).<br><br>CONCLUSION: The study revealed a significant correlation between intestinal microbiota abundance and cytokine levels, suggesting that gut microbiota disruption in OSAHS patients may be linked to systemic chronic inflammation.},
}
@article {pmid39372735,
year = {2024},
author = {Solazzo, G and Rovelli, S and Iodice, S and Chung, M and Frimpong, M and Bollati, V and Ferrari, L and Ghedin, E},
title = {The microbiome of Total Suspended Particles (TSP) and its influence on the respiratory microbiome of healthy office workers.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.08.12.607611},
pmid = {39372735},
issn = {2692-8205},
abstract = {Air particulate matter (PM) is widely recognized for its potential to negatively affect human health, including changes in the upper respiratory microbiome. However, research on PM-associated microbiota remains limited and mostly focused on PM (e.g., PM 2.5 and PM 10). This study aims to characterize for the first time the microbiome of Total Suspended Particles (TSP) and investigate the correlations of indoor TSP with the human upper respiratory microbiome. Biological and environmental samples were collected over three collection periods lasting three weeks each, between May and July 2022 at the University of Milan and the University of Insubria Como. TSP were sampled using a filter-based technique, while respiratory samples from both anterior nares (AN) and the nasopharynx (NP) were collected using swabs. Microbiome analysis of both human (N = 145) and TSP (N = 51) samples was conducted on metagenomic sequencing data. A comparison of indoor and outdoor TSP microbiomes revealed differences in microbial diversity and taxonomic composition. The indoor samples had higher relative abundance of environmental bacteria often associated with opportunistic infections like Paracoccus sp., as well as respiratory bacteria such as Staphylococcus aureus and Klebsiella pneumoniae . Additionally, both indoor and outdoor TSP samples contained broad spectrum antibiotic resistance genes. Indoor TSP exposure was negatively associated with commensal bacteria and positively associated with Staphylococcus aureus relative abundance. Finally, a correlation between the relative abundance of respiratory bacteria identified in the indoor TSP and the upper respiratory microbiome was found, suggesting a potential interaction between TSP and the upper airways.},
}
@article {pmid39372409,
year = {2024},
author = {Li, N and Zhao, J and Liu, Y and Zhang, Y},
title = {Dynamic findings of brain magnetic resonance imaging in a haploidentical hematopoietic stem cell transplantation recipient with cytomegalovirus ventriculoencephalitis: a case report and systematic review.},
journal = {Frontiers in immunology},
volume = {15},
number = {},
pages = {1450576},
pmid = {39372409},
issn = {1664-3224},
mesh = {Humans ; *Hematopoietic Stem Cell Transplantation/adverse effects ; Male ; *Cytomegalovirus Infections/diagnostic imaging ; Middle Aged ; *Magnetic Resonance Imaging ; Brain/diagnostic imaging/pathology/virology ; Cytomegalovirus/genetics ; Encephalitis, Viral/etiology/diagnostic imaging ; Transplantation, Haploidentical ; Antiviral Agents/therapeutic use ; Graft vs Host Disease/etiology ; Cerebral Ventriculitis/diagnostic imaging/etiology ; Precursor Cell Lymphoblastic Leukemia-Lymphoma/therapy ; Fatal Outcome ; },
abstract = {Our case demonstrated unique cytomegalovirus (CMV) encephalitis post-haploidentical donor hematopoietic stem cell transplantation (HID-HSCT), with early findings on diffusion-weighted brain magnetic resonance imaging (MRI) in the absence of any neurologic symptoms. A 54-year-old Chinese man with acute lymphoblastic leukemia (Philadelphia chromosome-negative) underwent HID-HSCT. After HSCT, the patient developed CMV viremia and severe acute graft-versus-host disease. Recurrence of CMV viremia was observed. On day 129, brain MRI was performed to determine the cause for the intermittent fever. Diffusion-weighted imaging (DWI) revealed several bright spots in the cortex of the frontal lobes and anterior angle of the left lateral ventricle. Subsequently, he developed transplant-associated thrombotic microangiopathy, posterior reversible encephalopathy syndrome, and enlargement of lesions alongside the ventricular wall on a brain MRI series. Metagenomic next-generation sequencing (NGS) of the cerebrospinal fluid (CSF) led to the final diagnosis of CMV encephalitis. Although ganciclovir combined with foscarnet was administered, the patient's consciousness deteriorated, followed by respiratory failure. The patient died on day 198. Additionally, we performed a systematic review to comprehensively analyze this disease. Regarding treatment, immunological therapies, including virus-specific T cells from a third donor and CMV-cytotoxic T lymphocytes, may be more effective. This case report and systematic review underscores the complexities of managing CMV ventriculoencephalitis in HSCT recipients and emphasizes the importance of early diagnosis by brain MRI and CSF polymerase chain reaction or NGS and ongoing research in improving outcomes.},
}
@article {pmid39372273,
year = {2024},
author = {Chen, Q and Chen, X and Mo, P and Chen, L and Du, Q and Hu, W and Jiang, Q and Zhang, Z and Zhang, Y and Guo, Q and Xiong, Y and Deng, L},
title = {Diagnostic values of BALF metagenomic next-generation sequencing, BALF real-time PCR and serum BDG for Pneumocystis jirovecii pneumonia in HIV-infected patients.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1421660},
pmid = {39372273},
issn = {1664-302X},
abstract = {INTRODUCTION: This study aimed to assess the diagnostic values of bronchoalveolar lavage fluid (BALF) real-time polymerase chain reaction (PCR) and BALF metagenomic next-generation sequencing (mNGS) for Pneumocystis jirovecii pneumonia (PJP) in patients infected with human immunodeficiency virus (HIV).<br><br>METHODS: A total of 99 HIV-infected PJP patients and 61 HIV-infected patients diagnosed with non-PJP pneumonia between March 2019 and December 2022 were enrolled. P. jirovecii and multiple other co-pathogens detected in BALF by mNGS were analyzed. The clinical final diagnosis was employed as a benchmark. We compared the diagnostic performance of mNGS in PJP with serum BDG and BALF real-time PCR. The mixed infections detected by mNGS and modifications of antimicrobial treatment were also analyzed.<br><br>RESULTS: The sensitivity of mNGS test of BALF samples reached 85.86%, which was significantly higher than serum BDG (39.39%, P < 0.001). The sensitivity of BALF P. jirovecii PCR (84.85%) was similar with mNGS (P > 0.05). The specificity of mNGS (100%) was also same as PCR (100.0%), and superior to serum BDG (88.52%, P < 0.001). Besides, mNGS performs remarkably well in identifying co-pathogens of PJP patients infected with HIV. In addition to P. jirovecii, 82 cases (82.83%) of other co-pathogens were identified based on mNGS. Moreover, thirty-four patients (34.34%) increased therapeutic dose of trimethoprim-sulfamethoxazole (TMP-SMZ) based on BALF P. jirovecii PCR. Based on the mNGS results, initial antimicrobial treatment was modified in 86.87% (86/99) of PJP patients.<br><br>CONCLUSION: BALF mNGS and real-time PCR are two powerful techniques for rapid diagnosis of PJP with high specificity and sensitivity. Moreover, the benefit of mNGS is that it may identify other organisms besides PJP and it may benefit proper and prompt treatment.},
}
@article {pmid39372272,
year = {2024},
author = {Jiang, C and Peng, F and Zhang, L and Zhang, Y and Wang, J and Li, J and Cui, B and Cao, C and Wang, C and Qin, Y and Wang, R and Zhao, Z and Jiang, J and Yang, M and Sun, M and Yang, L and Zhang, Q},
title = {Isolation, identification, and mechanism analysis of plant growth-promoting rhizobacteria in tobacco.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1457624},
pmid = {39372272},
issn = {1664-302X},
abstract = {Plant growth, crop yield, and pest and disease control are enhanced by PGPR (Plant growth promoting rhizobacteria), which are beneficial microorganisms found in a close symbiosis with plant roots. Phytohormones are secreted, nutrient uptake is improved, and soil properties along with the microbiological environment are regulated by these microorganisms, making them a significant focus in agricultural research. In this study, the efficient PGPR strain T1 was isolated and screened from tobacco inter-root soil, and identified and confirmed by ITS sequencing technology. Tobacco growth indicators and soil property changes were observed and recorded through potting experiments. The activities of key enzymes (e.g., sucrase, catalase, urease) in soil were further determined. High-throughput sequencing technology was utilized to sequence the soil microbial community, and combined with macro-genomics analysis, the effects of T1 strain on soil microbial diversity and metabolic pathways were explored. Following the application of T1, significant improvements were observed in the height, leaf length, and width of tobacco plants. Furthermore, the physical and chemical properties of the soil were notably enhanced, including a 26.26% increase in phosphorus availability. Additionally, the activities of key soil enzymes such as sucrase, catalase, and urease were significantly increased, indicating improved soil health and fertility. Comprehensive joint microbiomics and macrogenomics analyses revealed a substantial rise in the populations of beneficial soil microorganisms and an enhancement in metabolic pathways, including amino acid metabolism, synthesis, and production of secondary metabolites. These increase in beneficial microorganisms and the enhancement of their metabolic functions are crucial for plant growth and soil fertility. This study provides valuable references for the development of innovative microbial fertilizers and offers programs for the sustainable development of modern agriculture.},
}
@article {pmid39372270,
year = {2024},
author = {Zheng, X and Chen, M and Zhuang, Y and Zhao, L and Qian, Y and Shi, C},
title = {Unveiling genetic links between gut microbiota and asthma: a Mendelian randomization.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1448629},
pmid = {39372270},
issn = {1664-302X},
abstract = {BACKGROUND: Multiple studies suggest a potential connection between the gut microbiome and asthma. Our objective is to use advanced genetic and metagenomic techniques to elucidate the causal relationships and underlying mechanisms between gut microbiota and asthma.<br><br>METHODS: The study utilized comprehensive Linkage Disequilibrium Score Regression (LDSC) and Mendelian randomization (MR) analyses to examine the relationship between 119 gut microbiota genera and asthma, using publicly accessible genome-wide association studies (GWAS). The meta-analysis synthesized summary effect estimates obtained from LDSC, forward MR, and reverse MR. The MiBioGen collaboration, involving 18,340 individuals, identified genetic variations associated with gut bacteria. Asthma data were collected from the UK Biobank, FinnGen, and GERA, encompassing a total of 82,060 cases and 641,049 controls.<br><br>RESULTS: LDSC analysis revealed significant negative genetic correlations between asthma and RuminococcaceaeUCG004 (Rg&#x2009;=&#x2009;-0.55, p =&#x2009;7.66&#x2009;&#xd7;&#x2009;10[-5]) and Subdoligranulum (Rg&#x2009;=&#x2009;-0.35, p =&#x2009;3.61&#x2009;&#xd7;&#x2009;10[-4]). Forward MR analysis suggested associations between Butyricicoccus (OR&#x2009;=&#x2009;0.92, p =&#x2009;0.01), Turicibacter (OR&#x2009;=&#x2009;0.95, p =&#x2009;0.025), Butyrivibrio (OR&#x2009;=&#x2009;0.98, p =&#x2009;0.047), and reduced asthma risk. Conversely, Coprococcus2 (OR&#x2009;=&#x2009;1.10, p =&#x2009;0.035) and Roseburia (OR&#x2009;=&#x2009;1.07, p =&#x2009;0.039) were associated with increased risk. Reverse MR analysis indicated significant associations between genetically predicted asthma and Eubacteriumxylanophilumgroup (Beta&#x2009;=&#x2009;-0.08, p =&#x2009;9.25&#x2009;&#xd7;&#x2009;10[-7]), LachnospiraceaeNK4A136group (Beta&#x2009;=&#x2009;-0.05, p =&#x2009;1.26&#x2009;&#xd7;&#x2009;10[-4]), and Eisenbergiella (Beta&#x2009;=&#x2009;0.06, p =&#x2009;0.015, Rg_P =&#x2009;0.043).<br><br>CONCLUSION: The findings underscore significant genetic correlations and causal relationships between specific gut microbiota and asthma. These insights highlight the potential of gut microbiota as both markers and modulators of asthma risk, offering new avenues for targeted therapeutic strategies.},
}
@article {pmid39372268,
year = {2024},
author = {Wang, C and Hou, L and Jiang, N and Wang, Y and Mao, X and Zhou, P and Xia, Y and Wang, Y and Chen, C and Yang, X and Luo, Q and Pan, J},
title = {Microbial diversity in earthen site of exhibition Hall of pit no. 1 at the terracotta warriors Museum in Emperor Qinshihuang's mausoleum site museum and its correlation with environmental factors.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1378180},
pmid = {39372268},
issn = {1664-302X},
abstract = {INTRODUCTION: Earthen sites are essential cultural relic resources, and site museums are a fundamental component of China's cultural heritage protection. The mausoleum of the Qin Shi Huang Emperor is one of the largest, most peculiar, and richest imperial tombs in the world. The exhibition hall of the burial pit No. 1 of the Terra Cotta Warriors is the earliest exhibition hall built and opened to the public. However, after years of excavation and open exhibitions, the earthen site of the Emperor Qinshihuang's Mausoleum Site Museum has deteriorated to varying degrees due to changes in the modern environment. There is an urgent need to control microbial diseases and protect the earthen site.<br><br>METHODS: We analyzed the physical and chemical properties and bioindicators of the collected soil samples. We also established a metagenomic library and conducted a correlation analysis between microbial community composition and environmental factors. Cultivable fungi obtained from air and soil samples were identified, and allicin volatile gas fungistasis test was conducted.<br><br>RESULT: Research has found that four different areas of the exhibition hall have different types of microbial diseases owing to their different environments. The main pathogenic fungi in earthen site may lead to potential microbial diseases that affect important cultural relics such as the Terra Cotta Warriors. Penicillium, Aspergillus and Talaromyces showed relatively specific growth in relation to environmental factors and showed a better raw growth advantage.Allicin gas had a inhibitory effect on 12 types of fungi, therefore allicin gas had a potent inhibitory effect on the growth of the most culturable fungal hyphae.<br><br>DISCUSSION: This study provides basic data for the study of microbial diversity in the exhibition hall of Pit No. 1 at the Terracotta Warriors Museum in Emperor Qinshihuang's Mausoleum Site Museum. It provides a reference for future protection work, which is of great significance.},
}
@article {pmid39372067,
year = {2024},
author = {Liu, J and Shi, J and Zhang, T and Chen, M and Li, Z and Lu, C and Wang, F},
title = {Serum and Fecal Metabolite Profiles Linking With Gut Microbiome in Triple-Negative Breast Cancer Patients.},
journal = {Breast cancer : basic and clinical research},
volume = {18},
number = {},
pages = {11782234241285645},
pmid = {39372067},
issn = {1178-2234},
abstract = {BACKGROUND: Triple-negative breast cancer (TNBC) is a subtype of breast cancer characterized by poor prognosis due to the absence of effective targeted therapies. Emerging evidence indicates that the gut microbiota and its metabolites play a key role in the occurrence and development of TNBC. This study aimed to explore the metabolic changes and potential mechanisms associated with TNBC.<br><br>OBJECTIVES: This study aimed to explore the potential relationship between targeted metabolites and the gut microbiota in TNBC.<br><br>DESIGN: We recruited 8 participants, including 4 with TNBC and 4 with benign fibroadenomas as controls.<br><br>METHODS: The gut microbiota was analyzed using metagenomics on fecal samples. Liquid chromatography-mass spectrometry (LC-MS) was employed to identify differential metabolites in serum and fecal samples. The correlation between the gut microbiota and metabolites was analyzed using Spearman's correlation analysis.<br><br>RESULTS: Analysis of altered serum metabolites in the TNBC group revealed changes, particularly in carboxylic acids and derivatives, benzene, and substituted derivatives. Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway analysis revealed significant enrichment in 18 pathways. Regarding fecal metabolites, differences between the 2 groups also included carboxylic acids and derivatives, benzene, and substituted derivatives, with 28 metabolic pathways enriched based on KEGG pathway analysis. Metagenomics analysis showed differences in the relative abundance of Anaerococcus, Fischerella, and Schizosaccharomyces at the genus level, which have been previously associated with breast cancer. Furthermore, 4 serum metabolites-L-glutamine, citrate, creatinine, and creatine-along with 9 fecal metabolites, were associated with the aforementioned microbiota.<br><br>CONCLUSION: Our findings highlight distinct metabolite profiles in the serum and feces of patients with TNBC. The identification of gut microbiota and their associated metabolites provides new insights into the pathophysiological mechanisms underlying TNBC.},
}
@article {pmid39371578,
year = {2024},
author = {Zhang, J and Wang, Z and Jiang, Y and Zhang, D and Den, W and Wang, D and Peng, J and Li, J and Huang, W},
title = {A Case of Necrotizing Fasciitis/Myositis and Streptococcal Toxic Shock Syndrome Caused by emm22/ST46 Strain of Streptococcus pyogenes.},
journal = {Infection and drug resistance},
volume = {17},
number = {},
pages = {4251-4256},
pmid = {39371578},
issn = {1178-6973},
abstract = {Streptococcus pyogenes, also known as Group A Streptococcus (GAS), can cause severe invasive diseases with high fatality rates. We report a case of necrotizing fasciitis and myositis complicated by Streptococcal Toxic Shock-Like Syndrome (STSS) caused by the invasive emm22/ST46 strain of Streptococcus pyogenes in China. A previously healthy 57-year-old Chinese Canadian man presented with right calf pain and ulceration following a hike in the Gobi Desert, which progressed to unconsciousness and severe infection. Despite initial treatment, his condition deteriorated, leading to his transfer to our intensive care unit. Metagenomic Next-Generation Sequencing identified Streptococcus pyogenes, and antimicrobial susceptibility testing revealed resistance to erythromycin, tetracycline, and clindamycin. Despite broad-spectrum antimicrobial therapy, debridement, and supportive measures, the patient's condition necessitated amputation of the right lower limb. He recovered and was discharged from the hospital on Day 43. Whole-genome sequencing of the isolate identified 15 multiple virulence factors. Phylogenetic analysis revealed that the closest relative of the isolate was a strain identified in China. This case underscores the importance of early recognition and treatment of invasive GAS infections to prevent severe outcomes, and we should pay attention to invasive emm22/ST46 GAS infections in China.},
}
@article {pmid39371337,
year = {2024},
author = {Hu, X and Zhi, S and Wu, W and Tao, Y and Zhang, Y and Li, L and Li, X and Pan, L and Fan, H and Li, W},
title = {The application of metagenomics, radiomics and machine learning for diagnosis of sepsis.},
journal = {Frontiers in medicine},
volume = {11},
number = {},
pages = {1400166},
pmid = {39371337},
issn = {2296-858X},
abstract = {INTRODUCTION: Sepsis poses a serious threat to individual life and health. Early and accessible diagnosis and targeted treatment are crucial. This study aims to explore the relationship between microbes, metabolic pathways, and blood test indicators in sepsis patients and develop a machine learning model for clinical diagnosis.<br><br>METHODS: Blood samples from sepsis patients were sequenced. &#x3b1;-diversity and &#x3b2;-diversity analyses were performed to compare the microbial diversity between the sepsis group and the normal group. Correlation analysis was conducted on microbes, metabolic pathways, and blood test indicators. In addition, a model was developed based on medical records and radiomic features using machine learning algorithms.<br><br>RESULTS: The results of &#x3b1;-diversity and &#x3b2;-diversity analyses showed that the microbial diversity of sepsis group was significantly higher than that of normal group (p < 0.05). The top 10 microbial abundances in the sepsis and normal groups were Vitis vinifera, Mycobacterium canettii, Solanum pennellii, Ralstonia insidiosa, Ananas comosus, Moraxella osloensis, Escherichia coli, Staphylococcus hominis, Camelina sativa, and Cutibacterium acnes. The enriched metabolic pathways mainly included Protein families: genetic information processing, Translation, Protein families: signaling and cellular processes, and Unclassified: genetic information processing. The correlation analysis revealed a significant positive correlation (p < 0.05) between IL-6 and Membrane transport. Metabolism of other amino acids showed a significant positive correlation (p < 0.05) with Cutibacterium acnes, Ralstonia insidiosa, Moraxella osloensis, and Staphylococcus hominis. Ananas comosus showed a significant positive correlation (p < 0.05) with Poorly characterized and Unclassified: metabolism. Blood test-related indicators showed a significant negative correlation (p < 0.05) with microorganisms. Logistic regression (LR) was used as the optimal model in six machine learning models based on medical records and radiomic features. The nomogram, calibration curves, and AUC values demonstrated that LR performed best for prediction.<br><br>DISCUSSION: This study provides insights into the relationship between microbes, metabolic pathways, and blood test indicators in sepsis. The developed machine learning model shows potential for aiding in clinical diagnosis. However, further research is needed to validate and improve the model.},
}
@article {pmid39371172,
year = {2024},
author = {Akagbosu, CO and McCauley, KE and Namasivayam, S and Romero-Soto, HN and O'Brien, W and Bacorn, M and Bohrnsen, E and Schwarz, B and Mistry, S and Burns, AS and Perez-Chaparro, PJ and Chen, Q and LaPoint, P and Patel, A and Krausfeldt, LE and Subramanian, P and Sellers, BA and Cheung, F and Apps, R and Douagi, I and Levy, S and Nadler, EP and Hourigan, SK},
title = {Gut microbiome shifts in adolescents after sleeve gastrectomy with increased oral-associated taxa and pro-inflammatory potential.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.09.16.24313738},
pmid = {39371172},
abstract = {BACKGROUND: Bariatric surgery is highly effective in achieving weight loss in children and adolescents with severe obesity, however the underlying mechanisms are incompletely understood, and gut microbiome changes are unknown.<br><br>OBJECTIVES: 1) To comprehensively examine gut microbiome and metabolome changes after laparoscopic vertical sleeve gastrectomy (VSG) in adolescents and 2) to assess whether the microbiome/metabolome changes observed with VSG influence phenotype using germ-free murine models.<br><br>DESIGN: 1) A longitudinal observational study in adolescents undergoing VSG with serial stool samples undergoing shotgun metagenomic microbiome sequencing and metabolomics (polar metabolites, bile acids and short chain fatty acids) and 2) a human-to-mouse fecal transplant study.<br><br>RESULTS: We show adolescents exhibit significant gut microbiome and metabolome shifts several months after VSG, with increased alpha diversity and notably with enrichment of oral-associated taxa. To assess causality of the microbiome/metabolome changes in phenotype, pre-VSG and post-VSG stool was transplanted into germ-free mice. Post-VSG stool was not associated with any beneficial outcomes such as adiposity reduction compared pre-VSG stool. However, post-VSG stool exhibited an inflammatory phenotype with increased intestinal Th17 and decreased regulatory T cells. Concomitantly, we found elevated fecal calprotectin and an enrichment of proinflammatory pathways in a subset of adolescents post-VSG.<br><br>CONCLUSION: We show that in some adolescents, microbiome changes post-VSG may have inflammatory potential, which may be of importance considering the increased incidence of inflammatory bowel disease post-VSG.<br><br>Bariatric surgery is highly effective in achieving weight loss in children and adolescents with severe obesity, however the underlying mechanisms are incompletely understood, and gut microbiome changes are unknown.<br><br>WHAT THIS STUDY ADDS: Significant gut microbiome and metabolome shifts were found several months after vertical sleeve gastrectomy in adolescents, notably with enrichment of oral-associated taxa. Using human to germ-free mice fecal transplant studies, the post-surgery changes in the gut microbiome/metabolome were shown to have inflammatory potential. Furthermore, raised fecal calprotectin and inflammatory systemic pathways were seen in a subset of adolescents post-surgery.<br><br>These findings may be of importance given the growing recognition of an increased incidence of inflammatory bowel disease after bariatric surgery and warrants further investigation.},
}
@article {pmid39345650,
year = {2024},
author = {Bhamidipati, SV and Surathu, A and Chao, H and Agustinho, DP and Xiang, Q and Kottapalli, K and Santhanam, A and Momin, Z and Walker, K and Menon, VK and Weissenberger, G and Emerick, N and Mahjabeen, F and Meng, Q and Hu, J and Sucgang, R and Henke, D and Sedlazeck, FJ and Khan, Z and Metcalf, GA and Avadhanula, V and Piedra, PA and Ramani, S and Atmar, RL and Estes, MK and Petrosino, JF and Gibbs, RA and Muzny, DM and Cregeen, SJ and Doddapaneni, H},
title = {Complete Genomic Characterization of Global Pathogens, Respiratory Syncytial Virus (RSV), and Human Norovirus (HuNoV) Using Probe-based Capture Enrichment.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39345650},
issn = {2692-8205},
support = {U19 AI144297/AI/NIAID NIH HHS/United States ; },
abstract = {Respiratory syncytial virus (RSV) is the leading cause of lower respiratory tract infections in children worldwide, while human noroviruses (HuNoV) are a leading cause of epidemic and sporadic acute gastroenteritis. Generating full-length genome sequences for these viruses is crucial for understanding viral diversity and tracking emerging variants. However, obtaining high-quality sequencing data is often challenging due to viral strain variability, quality, and low titers. Here, we present a set of comprehensive oligonucleotide probe sets designed from 1,570 RSV and 1,376 HuNoV isolate sequences in GenBank. Using these probe sets and a capture enrichment sequencing workflow, 85 RSV positive nasal swab samples and 55 (49 stool and six human intestinal enteroids) HuNoV positive samples encompassing major subtypes and genotypes were characterized. The Ct values of these samples ranged from 17.0-29.9 for RSV, and from 20.2-34.8 for HuNoV, with some HuNoV having below the detection limit. The mean percentage of post-processing reads mapped to viral genomes was 85.1% for RSV and 40.8% for HuNoV post-capture, compared to 0.08% and 1.15% in pre-capture libraries, respectively. Full-length genomes were>99% complete in all RSV positive samples and >96% complete in 47/55 HuNoV positive samples-a significant improvement over genome recovery from pre-capture libraries. RSV transcriptome (subgenomic mRNAs) sequences were also characterized from this data. Probe-based capture enrichment offers a comprehensive approach for RSV and HuNoV genome sequencing and monitoring emerging variants.},
}
@article {pmid39369676,
year = {2024},
author = {Zhuang, Y and Liu, S and Xiao, J and Chen, T and Gao, D and Xu, Y and Jiang, W and Wang, J and Hou, G and Li, S and Zhao, X and Huang, Y and Li, S and Zhang, S and Li, M and Wang, W and Li, S and Cao, Z},
title = {Metagenomics reveals the characteristics and potential spread of microbiomes and virulence factor genes in the dairy cattle production system.},
journal = {Journal of hazardous materials},
volume = {480},
number = {},
pages = {136005},
doi = {10.1016/j.jhazmat.2024.136005},
pmid = {39369676},
issn = {1873-3336},
abstract = {Virulence factor genes (VFGs) pose a potential threat to ecological security and animal health, and have attracted increasing attention in the livestock industry. As one of the primary livestock types, dairy cattle may be an important source of VFG transmission. However, the distribution, transmission, and evolution of VFGs in the gastrointestinal tract and surrounding environment of dairy cattle remain unclear. In the present study, a total of 263 samples were collected from cows, calves, colostrum, farm wastewater, and soil. Metagenomics was conducted to analyze changes in the microbiome and VFGs characteristics in these ecological niches. The VFGs of the cows showed distinct differences between the rumen and feces, and were influenced by the region. The dominant VFG hosts was regulated by their microbial structure. Colostrum administration of cows increased VFG abundance in their newborn calf feces sharply and Enterobacteriaceae became the primary host. While diet was the primary driving force for the temporal variation in calf VFGs. For samples of the surrounding environment, water and soil had higher VFG concentrations and were more structurally stable. Moreover, extensive interactions between the mobile genetic elements and VFGs and gene mobile analysis map based on metagenomic binning both displayed the potential horizontal transfer ability of VFGs in the cows and environment. Our study revealed the prevalence, diffusion, and regulatory factors of VFGs in dairy cattle production systems, providing novel insights into reducing livestock VFGs and limiting their spread.},
}
@article {pmid39369510,
year = {2024},
author = {Fang, R and Wang, X and Han, Z and Pang, R and Wu, D and Tai, J and Ouyang, C and Zhan, M and Kim, H and Xie, B and Su, Y},
title = {Dynamic responses of the inter-microbial synergism and thermodynamic conditions attribute to the inhibition-and-relief effects of chitosan towards anaerobic digestion.},
journal = {Water research},
volume = {267},
number = {},
pages = {122569},
doi = {10.1016/j.watres.2024.122569},
pmid = {39369510},
issn = {1879-2448},
abstract = {Wide commercial applications of chitosan in food preservation and green packaging fields inevitably lead to the universal existence in food, as well as the food waste (FW) processing system. However, whether and how the chitosan, a class of biomacromolecule substances, lead to dysfunction of anaerobic digestion (AD) process of FW remains less understood. Herein, chitosan exhibited an inhibition-and-relief effect with the AD process proceeding, and 80 mg/g-FW of chitosan decreased the net methane yield of FW by 24.7 %. The dynamic effect was ascribed to the varied fates of chitosan and the coupling biotic/abiotic influencing on multi-steps. Chitosan enhanced substrate flocs agglomeration, restraining the release of organics to liquid phase and reducing the binding affinity to enzymes. Among the various microorganisms involved in different steps, chitosan severely inhibited aceticlastic and hydrogenotrophic methanogen at the levels of microbial abundance, activity and function. Genome-centric metagenomics analyses revealed that transient chitosan decreased the coenzyme-based synergism of various microbial taxa involved in acetic acid generation/consumption metabolisms, including syntrophic propionate-oxidizing bacteria, syntrophic butyrate-oxidizing bacteria and methanogen. With the elimination of chitosan, these inhibitions were relieved, and the accumulated acetic acid and the more favorable thermodynamic conditions finally attributed to the recovery of AD performance.},
}
@article {pmid39369508,
year = {2024},
author = {Jang, Y and Lee, SH and Kim, NK and Park, HD},
title = {Metagenomic analysis reveals abundance of mixotrophic, heterotrophic, and homoacetogenic bacteria in a hydrogen-based membrane biofilm reactor.},
journal = {Water research},
volume = {267},
number = {},
pages = {122564},
doi = {10.1016/j.watres.2024.122564},
pmid = {39369508},
issn = {1879-2448},
abstract = {Heterotrophic microorganisms are frequently observed in hydrogenotrophic denitrification systems and are presumed to contribute to their improved performance. However, their roles and metabolic pathways in the hydrogen-based membrane biofilm reactor (H2-MBfR) system remain unclear. The objective of this study was to elucidate the underlying mechanisms driving heterotrophic denitrification. For this purpose, metagenomic analysis was conducted on an H2-MBfR showing higher denitrification performance, focusing on the metabolic function of the microbial community. Functional genes related to H2 oxidation, organic carbon metabolism, and denitrification were the major targets of interest. This analysis revealed a substantial number of genes associated with the oxidation of organic carbon compounds in the biofilm, suggesting its potential for heterotrophic denitrification. Investigation of the genes of interest in metagenome-assembled genomes (MAGs) has demonstrated a predominance of mixotrophs or heterotrophs rather than obligate autotrophs. Notably, MAGs exhibiting the highest abundance of genes of interest were affiliated with Hydrogenophaga and Thauera, implying their significant role in denitrifying the H2-MBfR as mixotrophs utilizing both H2 and organic substrates. The identification of 11 MAGs, presumed to originate from homoacetogens suggested that acetate might contribute to the proliferation of heterotrophs. Based on these metagenomic findings, possible metabolic pathways were identified to explain heterotrophic denitrification within the H2-MBfR biofilms.},
}
@article {pmid39369255,
year = {2024},
author = {Figueroa-Gonzalez, PA and Bornemann, TLV and Hinzke, T and Maaß, S and Trautwein-Schult, A and Starke, J and Moore, CJ and Esser, SP and Plewka, J and Hesse, T and Schmidt, TC and Schreiber, U and Bor, B and Becher, D and Probst, AJ},
title = {Metaproteogenomics resolution of a high-CO2 aquifer community reveals a complex cellular adaptation of groundwater Gracilibacteria to a host-dependent lifestyle.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {194},
pmid = {39369255},
issn = {2049-2618},
support = {CRC 1439/1 426547801//German Research Foundation (DFG)/ ; CRC 1439/1 426547801//German Research Foundation (DFG)/ ; },
mesh = {*Groundwater/microbiology ; Carbon Dioxide/metabolism ; Metagenomics ; Bacteria/genetics/classification/isolation &amp; purification/metabolism ; Germany ; Genome, Bacterial ; Phylogeny ; Microbiota/genetics ; Proteogenomics ; Adaptation, Physiological ; Proteomics ; },
abstract = {BACKGROUND: Bacteria of the candidate phyla radiation (CPR), constituting about 25% of the bacterial biodiversity, are characterized by small cell size and patchy genomes without complete key metabolic pathways, suggesting a symbiotic lifestyle. Gracilibacteria (BD1-5), which are part of the CPR branch, possess alternate coded genomes and have not yet been cultivated. The lifestyle of Gracilibacteria, their temporal dynamics, and activity in natural ecosystems, particularly in groundwater, has remained largely unexplored. Here, we aimed to investigate Gracilibacteria activity in situ and to discern their lifestyle based on expressed genes, using the metaproteogenome of Gracilibacteria as a function of time in the cold-water geyser Wallender Born in the Volcanic Eifel region in Germany.<br><br>RESULTS: We coupled genome-resolved metagenomics and metaproteomics to investigate a cold-water geyser microbial community enriched in Gracilibacteria across a 12-day time-series. Groundwater was collected and sequentially filtered to fraction CPR and other bacteria. Based on 725 Gbps of metagenomic data, 1129 different ribosomal protein S3 marker genes, and 751 high-quality genomes (123 population genomes after dereplication), we identified dominant bacteria belonging to Gallionellales and Gracilibacteria along with keystone microbes, which were low in genomic abundance but substantially contributing to proteomic abundance. Seven high-quality Gracilibacteria genomes showed typical limitations, such as limited amino acid or nucleotide synthesis, in their central metabolism but no co-occurrence with potential hosts. The genomes of these Gracilibacteria were encoded for a high number of proteins involved in cell to cell interaction, supporting the previously surmised host-dependent lifestyle, e.g., type IV and type II secretion system subunits, transporters, and features related to cell motility, which were also detected on protein level.<br><br>CONCLUSIONS: We here identified microbial keystone taxa in a high-CO2 aquifer, and revealed microbial dynamics of Gracilibacteria. Although Gracilibacteria in this ecosystem did not appear to target specific organisms in this ecosystem due to lack of co-occurrence despite enrichment on 0.2-&#xb5;m filter fraction, we provide proteomic evidence for the complex machinery behind the host-dependent lifestyle of groundwater Gracilibacteria. Video Abstract.},
}
@article {pmid39369191,
year = {2024},
author = {Zhao, J and Sun, Y and Tang, J and Guo, K and Wang, K and Zhuge, J and Fang, H},
title = {The clinical application of metagenomic next-generation sequencing in immunocompromised patients with severe respiratory infections in the ICU.},
journal = {Respiratory research},
volume = {25},
number = {1},
pages = {360},
pmid = {39369191},
issn = {1465-993X},
support = {No. 2023KY1296//Medical and Health Research Program of Zhejiang Province/ ; },
mesh = {Humans ; Male ; *Immunocompromised Host ; Female ; *Intensive Care Units ; Middle Aged ; *High-Throughput Nucleotide Sequencing/methods ; Aged ; *Metagenomics/methods ; *Respiratory Tract Infections/microbiology/diagnosis/drug therapy/immunology/mortality ; Bronchoalveolar Lavage Fluid/microbiology ; Adult ; Retrospective Studies ; Severity of Illness Index ; Anti-Bacterial Agents/therapeutic use ; },
abstract = {BACKGROUND: Early targeted antibiotic therapy is crucial for improving the prognosis of immunocompromised patients with severe respiratory infections (SRIs) in the intensive care unit (ICU). Metagenomic next-generation sequencing (mNGS) has shown significant value in pathogen detection, but research on lower respiratory tract microorganisms remains limited.<br><br>METHODS: This study enrolled 234 patients with SRIs in the ICU, and individuals were categorized into immunocompromised and immunocompetent groups. We compared the diagnostic performance of mNGS using bronchoalveolar lavage fluid (BALF) with conventional microbiological tests (CMTs) and analyzed the value of mNGS in immunocompromised patients with SRIs in the ICU.<br><br>RESULTS: Among all patients, the pathogenic microorganism detection rate of mNGS was higher than that of CMTs (94.02% vs 66.67%, P&#x2009;<&#x2009;0.05), both in the immunocompromised group (95.0% vs 58.75%, P&#x2009;<&#x2009;0.05) and the immunocompetent group (93.51% vs 71.43%, P&#x2009;<&#x2009;0.05). mNGS detected more pathogens than CMTs did (167 vs 51), identifying 116 organisms that were missed by CMTs. The proportion of antibiotic regimen adjustments based on mNGS results was significantly higher compared to CMTs in both the immunocompromised (70.00% vs 17.50%, P&#x2009;<&#x2009;0.05) and immunocompetent groups (48.70% vs 15.58%, P&#x2009;<&#x2009;0.05). In the immunocompromised group, patients who had their antibiotic treatment adjusted on mNGS results had improved prognosis, with significantly lower ICU mortality (8.93% vs 50%, P&#x2009;<&#x2009;0.05) and 28-day mortality rates (30.36% vs 68.75%, P&#x2009;<&#x2009;0.05) than CMTs. In the immunocompetent group, no statistically significant differences were observed in ICU mortality or 28-day mortality (20.00% vs 33.33%, P&#x2009;>&#x2009;0.05; 42.67% vs 45.83%, P&#x2009;>&#x2009;0.05).<br><br>CONCLUSION: mNGS shows significant value in detecting pathogens in immunocompromised patients with SRIs in ICU. For immunocompromised patients who respond poorly to empirical treatment, mNGS can provide an etiological basis, helping adjust antibiotic regimens more precisely and thereby improving patient prognosis.},
}
@article {pmid39368785,
year = {2024},
author = {Malan-Müller, S and Martín-Hernández, D and Caso, JR and Matthijnssens, J and Rodriguez-Urrutia, A and Lowry, CA and Leza, JC},
title = {Metagenomic symphony of the intestinal ecosystem: How the composition affects the mind.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bbi.2024.09.033},
pmid = {39368785},
issn = {1090-2139},
abstract = {Mental health disorders and neurodegenerative diseases place a heavy burden on patients and societies, and, although great strides have been made to understand the pathophysiology of these conditions, advancement in drug development is lagging. The importance of gastrointestinal health in maintaining overall health and preventing disease is not a new concept. Hundreds of years ago, healers from various cultures and civilizations recognized the crucial role of the gut in sustaining health. More than a century ago, scientists began exploring the restorative effects of probiotics, marking the early recognition of the importance of gut microbes. The omics era brought more enlightenment and enabled researchers to identify the complexity of the microbial ecosystems we harbour, encompassing bacteria, eukaryotes (including fungi), archaea, viruses, and other microorganisms. The extensive genetic capacity of the microbiota is dynamic and influenced by the environment. The microbiota therefore serves as a significant entity within us, with evolutionarily preserved functions in host metabolism, immunity, development, and behavior. The significant role of the bacterial gut microbiome in mental health and neurodegenerative disorders has been realized and described within the framework of the microbiota-gut-brain axis. However, the bacterial members do not function unaccompanied, but rather in concert, and there is a substantial knowledge gap regarding the involvement of non-bacterial microbiome members in these disorders. In this review, we will explore the current literature that implicates a role for the entire metagenomic ensemble, and how their complex interkingdom relationships could influence CNS functioning in mental health disorders and neurodegenerative diseases.},
}
@article {pmid39368784,
year = {2024},
author = {McCoubrey, LE and Shen, C and Mwasambu, S and Favaron, A and Sangfuang, N and Thomaidou, S and Orlu, M and Globisch, D and Basit, AW},
title = {Characterising and preventing the gut microbiota's inactivation of trifluridine, a colorectal cancer drug.},
journal = {European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences},
volume = {},
number = {},
pages = {106922},
doi = {10.1016/j.ejps.2024.106922},
pmid = {39368784},
issn = {1879-0720},
abstract = {The gut microbiome can metabolise hundreds of drugs, potentially affecting their bioavailability and pharmacological effect. As most gut bacteria reside in the colon, drugs that reach the colon in significant proportions may be most impacted by microbiome metabolism. In this study the anti-colorectal cancer drug trifluridine was used as a model drug for characterising metabolism by the colonic microbiota, identifying correlations between bacterial species and individuals' rates of microbiome drug inactivation, and developing strategies to prevent drug inactivation following targeted colonic delivery. High performance liquid chromatography and ultra-high performance liquid chromatography coupled with high resolution tandem mass spectrometry demonstrated trifluridine's variable and multi-route metabolism by the faecal microbiota sourced from six healthy humans. Here, four drug metabolites were linked to the microbiome for the first time. Metagenomic sequencing of the human microbiota samples revealed their composition, which facilitated prediction of individual donors' microbial trifluridine inactivation. Notably, the abundance of Clostridium perfringens strongly correlated with the extent of trifluridine inactivation by microbiota samples after 2 hours (R[2] = 0.8966). Finally, several strategies were trialled for the prevention of microbial trifluridine metabolism. It was shown that uridine, a safe and well-tolerated molecule, significantly reduced the microbiota's metabolism of trifluridine by acting as a competitive enzyme inhibitor. Further, uridine was found to provide prebiotic effects. The findings in this study greatly expand knowledge on trifluridine's interactions with the gut microbiome and provide valuable insights for investigating the microbiome metabolism of other drugs. The results demonstrate how protection strategies could enhance the colonic stability of microbiome-sensitive drugs.},
}
@article {pmid39368548,
year = {2024},
author = {Navanandan, N and Jackson, ND and Hamlington, KL and Everman, JL and Pruesse, E and Secor, EA and Stewart, Z and Diener, K and Hardee, I and Edid, A and Sulbaran, H and Mistry, RD and Florin, TA and Yoder, AC and Moore, CM and Szefler, SJ and Liu, AH and Seibold, MA},
title = {Viral Determinants of Childhood Asthma Exacerbation Severity and Treatment Response.},
journal = {The journal of allergy and clinical immunology. In practice},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaip.2024.09.020},
pmid = {39368548},
issn = {2213-2201},
abstract = {BACKGROUND: Although respiratory viruses are common triggers of asthma exacerbations, the influence of viral infection characteristics on exacerbation presentation and treatment response in the pediatric emergency department (ED) is unclear.<br><br>OBJECTIVE: To assess viral infection characteristics of children experiencing ED asthma exacerbations and to test their associations with severity and treatment response.<br><br>METHODS: Prospective study of children, 4-18 years, who received standard ED asthma exacerbation treatment with inhaled bronchodilators and systemic corticosteroids. Nasal swabs collected for viral metagenomic analyses determined virus presence, load and species. Outcomes included exacerbation severity (Pediatric Asthma Severity (PAS) score, clinician impression, and vital signs) and treatment response (discharge home without needing additional asthma therapies).<br><br>RESULTS: Of 107 children, 47% had moderate/severe exacerbations by PAS and 64% demonstrated treatment response. Viral metagenomic analysis on nasal swabs from 73 children detected virus in 86%, with 10 different species identified, primarily rhinovirus A (RV-A), RV-C, and enterovirus D68. Exacerbations involving RV-A were milder (odds ratio [OR]=0.25; 95% CI=0.07-0.83) and tended to be more responsive to treatment compared to non-RV-A infections, whereas exacerbations involving enterovirus D68 were more severe (OR=8.3; 95% CI=1.3-164.7) and had no treatment response association. Viral load was not associated with treatment response but exhibited a strong linear relationship with heart rate (rpartial=0.48), respiratory rate (rpartial=0.25), and oxygen saturation (rpartial=-0.25), indicative of severity.<br><br>CONCLUSIONS: The majority of ED asthma exacerbations are triggered by respiratory viruses. Viral species are associated with severity and treatment response, suggesting early pathogen detection could inform ED treatment decisions. Additional studies are needed to identify differences in pathobiology underlying exacerbations triggered by different viral species, and how to effectively treat these heterogeneous exacerbations.},
}
@article {pmid39368512,
year = {2024},
author = {Niu, X and Lin, L and Zhang, T and An, X and Li, Y and Yu, Y and Hong, M and Shi, H and Ding, L},
title = {Research on antibiotic resistance genes in wild and artificially bred green turtles (Chelonia mydas).},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {176716},
doi = {10.1016/j.scitotenv.2024.176716},
pmid = {39368512},
issn = {1879-1026},
abstract = {Sea turtles, vital to marine ecosystems, face population decline. Artificial breeding is a recovery strategy, yet it risks introducing antibiotic resistance genes (ARGs) to wild populations and ecosystems. This study employed metagenomic techniques to compare the distribution characteristics of ARGs in the guts of wild and artificially bred green turtles (Chelonia mydas). The findings revealed that the total abundance of ARGs in C. mydas that have been artificially bred was significantly higher than that in wild individuals. Additionally, the abundance of mobile genetic elements (MGEs) co-occurring with ARGs in artificially bred C. mydas was significantly higher than in wild C. mydas. In the analysis of bacteria carrying ARGs, wild C. mydas exhibited greater bacterial diversity. Furthermore, in artificially bred C. mydas, we discovered 23 potential human pathogenic bacteria (HPB) that contain antibiotic resistance genes. In contrast, in wild C. mydas, only one type of HPB carrying an antibiotic resistance gene was found. The findings of this study not only enhance our understanding of the distribution and dissemination of ARGs within the gut microbial communities of C. mydas, but also provide vital information for assessing the potential impact of releasing artificially bred C. mydas on the spread of antibiotic resistance.},
}
@article {pmid39368509,
year = {2024},
author = {Wen, M and Liu, Y and Yang, C and Dou, Y and Zhu, S and Tan, G and Wang, J},
title = {Effects of manure and nitrogen fertilization on soil microbial carbon fixation genes and associated communities in the Loess Plateau of China.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {176581},
doi = {10.1016/j.scitotenv.2024.176581},
pmid = {39368509},
issn = {1879-1026},
abstract = {The effects of long-term fertilization on soil carbon (C) cycling have been a key focus of agricultural sustainable development research. However, the influences of different fertilization treatments on soil microbial C fixation profiles are still unclear. Metagenomics technology and multivariate analysis were employed to inquire changes in soil properties, soil microbial C fixation genes and associated bacterial communities, and the influence of dominant soil properties on C fixation genes. The contents of soil C and nitrogen fractions were signicficantly higher in manure or combined with nitrogen fertilization (NM) than other treatments. The composition of soil microbial C fixation genes and associated bacterial communities varied among different fertilization treatments. Compared with other treatments, the total abundance of microbial C fixation genes and the abundance of Proteobacteria were significantly higher in NM than in other treatments, as well as the abundances of C fixation genes involved in dicarboxylate/4-hydroxybutyrate cycle and reductive citrate cycle. Key functional genes and main bacterial communities presented in the middle of the co-occurrence network. Soil organic carbon, total nitrogen, and microbial biomass nitrogen were the dominant soil properties influencing microbial C fixation genes and associated bacterial communitis. Fertilization increased the abundance of C fixation genes by affecting the changes in bacterial communities abundance mediated by soil properties. Overall, elucidating the responses of soil microbial C fixation genes and associated communities to different fertilization will enhance our understanding of the processes of soil C fixation in farmland.},
}
@article {pmid39368386,
year = {2024},
author = {Wang, W and Wang, X and Zhi, R and Zhang, L and Lei, S and Farooq, A and Yan, W and Song, Z and Zhang, C},
title = {Microbial mechanisms for CO2 and CH4 emissions in Robinia pseudoacacia forests along a North-South transect in the Loess Plateau.},
journal = {Journal of environmental management},
volume = {370},
number = {},
pages = {122802},
doi = {10.1016/j.jenvman.2024.122802},
pmid = {39368386},
issn = {1095-8630},
abstract = {Forest soil microbes play a crucial role in regulating atmospheric-soil carbon fluxes. Environmental heterogeneity across forest types and regions may lead to differences in soil CO2 and CH4 emissions. However, the microbial mechanisms underlying these emission variations are currently unclear. In this study, we measured CO2 and CH4 emissions of Robinia pseudoacacia forests along a north-south transect in the Loess Plateau. Using metagenomic sequencing, we investigated the structural and functional profiles of soil carbon cycling microbial communities. Results indicated that the forest CO2 emissions of Robinia pseudoacacia was significantly higher in the north region than in the south region, while the CH4 emission was oppositely. This is mainly attributed to changes in gene abundance driven by soil pH and moisture in participating carbon degradation and methane oxidation processes across different forest regions. The gene differences in carbon fixation processes between regions primarily stem from the Calvin cycle, where the abundance of rbcL, rbcS, and prkB genes dominates microbial carbon fixation in forest soils. Random forest models revealed key genes involved in predicting forest soil CO2 emissions, including SGA1 and amyA for starch decomposition, TYR for lignin decomposition, chitinase for chitin decomposition, and pectinesterase for pectin decomposition. Microbial functional characterization revealed that interregional differences in CH4 emissions during methane metabolism may originate from methane oxidation processes, and the associated gene abundances (glyA, ppc, and pmoB) were key genes for predicting CH4 emissions from forest soils. Our results provide new insights into the microbial mechanisms of CO2 and CH4 emissions from forest soils, which will be crucial for accurate prediction of the forest soil carbon cycle in the future.},
}
@article {pmid39368357,
year = {2024},
author = {Zhao, Y and Zhao, Q and Liu, D and Xie, H and Zhang, J and Zheng, Y and Xu, X and Wu, H and Hu, Z},
title = {Antibiotic resistomes and ecological risk elimination in field-scale constructed wetland revealed by integrated metagenomics and metatranscriptomics.},
journal = {Journal of hazardous materials},
volume = {480},
number = {},
pages = {136045},
doi = {10.1016/j.jhazmat.2024.136045},
pmid = {39368357},
issn = {1873-3336},
abstract = {Constructed wetlands (CWs) are identified as significant ecological systems for the potential control of antibiotic resistance genes (ARGs) in the environment. However, the precise mechanisms governing removal, persistence, expression, and associated risks of ARGs during wetland treatment remain poorly understood. In this study, the distribution, mobility, expression, and hosts of ARGs in water, sediments, and plants of a field-scale CW and its parallel natural river were systematically investigated through metagenomic and metatranscriptomic approaches. Results showed that both the abundance and diversity of ARGs in water gradually decreased along the way of CW, reaching a final abundance removal rate of 72.28 % in the effluent. Source tracking analysis indicted that the reduction of ARGs in water was mainly achieved by the dynamic accumulation of ARGs in sediments and plants of the CW. Proteobacteria were identified as primary hosts for ARGs, particularly in sediments and plants during CW treatment. Moreover, although ESKAPE pathogens carrying multiple ARGs persisted in all media throughout the CW treatment, ARG expression levels and risk of water were also significantly decreased after CW treatment. Collectively, our comprehensive multi-omics study would enhance the understanding of ARG removal by CWs, offering insights for controlling antimicrobial resistance in wastewater treatment system.},
}
@article {pmid39367927,
year = {2024},
author = {Wang, Q and Wang, M and Chen, Y and Miao, Q and Jin, W and Ma, Y and Pan, J and Hu, B},
title = {Deciphering microbiome and fungi-bacteria interactions in chronic wound infections using metagenomic sequencing.},
journal = {European journal of clinical microbiology &amp; infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {},
number = {},
pages = {},
pmid = {39367927},
issn = {1435-4373},
support = {20YF1407700//Science and Technology Innovation Plan Of Shanghai Science and Technology Commission/ ; },
abstract = {PURPOSE: Chronic wounds caused by infections impose a considerable global healthcare burden. The microbial features of these infections and possible correlations between bacteria and fungi may influence wound healing. However, metagenomic next-generation sequencing (mNGS) analyses of these features remain sparse. Therefore, we performed mNGS on chronic wound infection samples to investigate features and correlations between the bacteriome and mycobiome in 66 patients (28: chronic wounds; 38: non-chronic wounds).<br><br>METHODS: Microbial community characteristics in patients with wound infections, microbiome-systemic inflammation associations, and bacteria-fungi correlations were analyzed.<br><br>RESULTS: Infections constituted the primary cause of wounds in this study. Nontuberculous mycobacteria (23%) and Mycobacterium tuberculosis (13%) were the most common pathogens associated with chronic wounds, whereas Staphylococcus aureus (15%) was the most prevalent in non-chronic wound infections. Patients with chronic wound infections had a higher abundance of Pseudomonas aeruginosa than those without chronic wounds. Microbes with a high relative abundance in chronic wound infections were less significantly associated with plasma inflammatory factors than those in non-chronic wound infections. Additionally, a positive correlation between Candida glabrata and P. aeruginosa and an association between Malassezia restricta and anaerobic species were detected in patients with chronic wound infections.<br><br>CONCLUSION: Our results further support the hypothesis that P. aeruginosa is a microbial biomarker of chronic wound infection regardless of the causative pathogens. Moreover, we propose a positive correlation between C. glabrata and P. aeruginosa in chronic wound infections, which advances the current understanding of fungi-bacteria correlations in patients with chronic wound infections.},
}
@article {pmid39367538,
year = {2024},
author = {Kong, Y and Zhang, R and Blain, S and Obernosterer, I},
title = {Seasonal dynamics in microbial trace metals transporters during phytoplankton blooms in the Southern Ocean.},
journal = {Environmental microbiology},
volume = {26},
number = {10},
pages = {e16695},
doi = {10.1111/1462-2920.16695},
pmid = {39367538},
issn = {1462-2920},
support = {202106230202//China Scholarship Council/ ; //Institut Polaire Fran&#xe7;ais Paul Emile Victor/ ; //Centre National de la Recherche Scientifique/ ; //Climate Initiative of the BNP Paribas Foundation/ ; },
mesh = {*Phytoplankton/metabolism/genetics/classification/growth &amp; development ; *Seasons ; *Bacteria/classification/metabolism/genetics ; *Trace Elements/metabolism ; Oceans and Seas ; Seawater/microbiology ; Metagenome ; Membrane Transport Proteins/genetics/metabolism ; Eutrophication ; Phylogeny ; },
abstract = {Trace metals are required as cofactors in metalloproteins that are essential in microbial metabolism and growth. The microbial requirements of diverse metals and the capabilities of prokaryotic taxa to acquire these metals remain poorly understood. We present here results from metagenomic observations over an entire productive season in the region off Kerguelen Island (Indian Sector of the Southern Ocean). We observed seasonal patterns in the abundance of prokaryotic transporters of seven trace elements (zinc [Zn], manganese [Mn], nickel [Ni], molybdenum [Mo], tungsten [W], copper [Cu] and cobalt [Co]) and the consecutive spring and summer phytoplankton blooms were strong drivers of these temporal trends. Taxonomic affiliation of the functional genes revealed that Rhodobacteraceae had a broad repertoire of trace metal transporters (Mn, Zn, Ni, W and Mo) and a more restricted set was observed for other prokaryotic groups, such as Flavobacteriaceae (Zn), Nitrincolaceae (Ni and W) and Thioglobaceae (Mo). The prevalence of trace metal transporters within a prokaryotic group, as determined on the family level, was overall confirmed in representative metagenome-assembled genomes. We discuss the potential involvement of prokaryotic groups in processes related to organic matter utilisation that require these metals and the consequences on carbon and trace metal cycling in surface waters of the Southern Ocean.},
}
@article {pmid39367431,
year = {2024},
author = {Gaber, M and Wilson, AS and Millen, AE and Hovey, KM and LaMonte, MJ and Wactawski-Wende, J and Ochs-Balcom, HM and Cook, KL},
title = {Visceral adiposity in postmenopausal women is associated with a pro-inflammatory gut microbiome and immunogenic metabolic endotoxemia.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {192},
pmid = {39367431},
issn = {2049-2618},
support = {W81XWH-20-1-0014//Congressionally Directed Medical Research Programs/ ; W81XWH-20-1-0014//Congressionally Directed Medical Research Programs/ ; W81XWH-20-1-0014//Congressionally Directed Medical Research Programs/ ; R01 DE013505, R01 DE024523/DE/NIDCR NIH HHS/United States ; R01 DE013505, R01 DE024523/DE/NIDCR NIH HHS/United States ; R01 DE013505, R01 DE024523/DE/NIDCR NIH HHS/United States ; R01 DE013505, R01 DE024523/DE/NIDCR NIH HHS/United States ; R01 DE013505, R01 DE024523/DE/NIDCR NIH HHS/United States ; HHSN268201600018C, HHSN268201600001C, HHSN268201600002C, HHSN268201600003C, and HHSN268201600004C/HL/NHLBI NIH HHS/United States ; HHSN268201600018C, HHSN268201600001C, HHSN268201600002C, HHSN268201600003C, and HHSN268201600004C/HL/NHLBI NIH HHS/United States ; },
mesh = {Female ; *Gastrointestinal Microbiome/drug effects ; *Endotoxemia/immunology/microbiology ; Humans ; *Postmenopause ; Animals ; Aged ; Mice ; *Lipopolysaccharides ; Intra-Abdominal Fat/metabolism/immunology ; Inflammation ; Aged, 80 and over ; Mice, Inbred C57BL ; Adiposity ; Bacteria/classification/isolation &amp; purification/metabolism/genetics ; Acute-Phase Proteins/metabolism ; Feces/microbiology ; Obesity, Abdominal/microbiology/immunology ; Absorptiometry, Photon ; Carrier Proteins ; Membrane Glycoproteins ; },
abstract = {BACKGROUND: Obesity, and in particular abdominal obesity, is associated with an increased risk of developing a variety of chronic diseases. Obesity, aging, and menopause are each associated with differential shifts in the gut microbiome. Obesity causes chronic low-grade inflammation due to increased lipopolysaccharide (LPS) levels which is termed "metabolic endotoxemia." We examined the association of visceral adiposity tissue (VAT) area, circulating endotoxemia markers, and the gut bacterial microbiome in a cohort of aged postmenopausal women.<br><br>METHODS: Fifty postmenopausal women (mean age 78.8&#x2009;&#xb1;&#x2009;5.3&#xa0;years) who had existing adipose measurements via dual x-ray absorptiometry (DXA) were selected from the extremes of VAT: n&#x2009;=&#x2009;25 with low VAT area (45.6&#x2009;&#xb1;&#x2009;12.5 cm[2]) and n&#x2009;=&#x2009;25 with high VAT area (177.5&#x2009;&#xb1;&#x2009;31.3 cm[2]). Dietary intake used to estimate the Healthy Eating Index (HEI) score was assessed with a food frequency questionnaire. Plasma LPS, LPS-binding protein (LBP), anti-LPS antibodies, anti-flagellin antibodies, and anti-lipoteichoic acid (LTA) antibodies were measured by ELISA. Metagenomic sequencing was performed on fecal DNA. Female C57BL/6 mice consuming a high-fat or low-fat diet were treated with 0.4&#xa0;mg/kg diet-derived fecal isolated LPS modeling metabolic endotoxemia, and metabolic outcomes were measured after 6&#xa0;weeks.<br><br>RESULTS: Women in the high VAT group showed increased Proteobacteria abundance and a lower Firmicutes/Bacteroidetes ratio. Plasma LBP concentration was positively associated with VAT area. Plasma anti-LPS, anti-LTA, and anti-flagellin IgA antibodies were significantly correlated with adiposity measurements. Women with high VAT showed significantly elevated LPS-expressing bacteria compared to low VAT women. Gut bacterial species that showed significant associations with both adiposity and inflammation (anti-LPS IgA and LBP) were Proteobacteria (Escherichia coli, Shigella spp., and Klebsiella spp.) and Veillonella atypica. Healthy eating index (HEI) scores negatively correlated with % body fat and anti-LPS IgA antibodies levels. Preclinical murine model showed that high-fat diet-fed mice administered a low-fat diet fecal-derived LPS displayed reduced body weight, decreased % body fat, and improved glucose tolerance test parameters when compared with saline-injected or high-fat diet fecal-derived LPS-treated groups consuming a high-fat diet.<br><br>CONCLUSIONS: Increased VAT in postmenopausal women is associated with elevated gut Proteobacteria abundance and immunogenic metabolic endotoxemia markers. Low-fat diet-derived fecal-isolated LPS improved metabolic parameters in high-fat diet-fed mice giving mechanistic insights into potential pro-health signaling mediated by under-acylated LPS isoforms. Video Abstract.},
}
@article {pmid39367251,
year = {2024},
author = {Zheng, J and Sun, Q and Zhang, M and Liu, C and Su, Q and Zhang, L and Xu, Z and Lu, W and Ching, J and Tang, W and Cheung, CP and Hamilton, AL and Wilson O'Brien, AL and Wei, SC and Bernstein, CN and Rubin, DT and Chang, EB and Morrison, M and Kamm, MA and Chan, FKL and Zhang, J and Ng, SC},
title = {Noninvasive, microbiome-based diagnosis of inflammatory bowel disease.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
pmid = {39367251},
issn = {1546-170X},
support = {R4030-22//Research Grants Council, University Grants Committee (RGC, UGC)/ ; 14121322//Research Grants Council, University Grants Committee (RGC, UGC)/ ; 2017PG-IBD003//Leona M. and Harry B. Helmsley Charitable Trust (Helmsley Charitable Trust)/ ; 10210816//Food and Health Bureau of the Government of the Hong Kong Special Administrative Region | Health and Medical Research Fund (HMRF)/ ; 82100573//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Despite recent progress in our understanding of the association between the gut microbiome and inflammatory bowel disease (IBD), the role of microbiome biomarkers in IBD diagnosis remains underexplored. Here we developed a microbiome-based diagnostic test for IBD. By utilization of metagenomic data from 5,979 fecal samples with and without IBD from different geographies and ethnicities, we identified microbiota alterations in IBD and selected ten and nine bacterial species for construction of diagnostic models for ulcerative colitis and Crohn's disease, respectively. These diagnostic models achieved areas under the curve >0.90 for distinguishing IBD from controls in the discovery cohort, and maintained satisfactory performance in transethnic validation cohorts from eight populations. We further developed a multiplex droplet digital polymerase chain reaction test targeting selected IBD-associated bacterial species, and models based on this test showed numerically higher performance than fecal calprotectin in discriminating ulcerative colitis and Crohn's disease from controls. Here we discovered universal IBD-associated bacteria and show the potential applicability of a multibacteria biomarker panel as a noninvasive tool for IBD diagnosis.},
}
@article {pmid39367018,
year = {2024},
author = {Baldi, A and Braat, S and Hasan, MI and Bennett, C and Barrios, M and Jones, N and Abdul Azeez, I and Wilcox, S and Roy, PK and Bhuiyan, MSA and Ataide, R and Clucas, D and Larson, LM and Hamadani, J and Zimmermann, M and Bowden, R and Jex, A and Biggs, BA and Pasricha, SR},
title = {Effects of iron supplements and iron-containing micronutrient powders on the gut microbiome in Bangladeshi infants: a randomized controlled trial.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {8640},
pmid = {39367018},
issn = {2041-1723},
support = {GNT1158696//Department of Health | National Health and Medical Research Council (NHMRC)/ ; GNT2009047//Department of Health | National Health and Medical Research Council (NHMRC)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/genetics ; Infant ; Bangladesh ; *Dietary Supplements ; *Micronutrients/administration &amp; dosage ; Female ; *Iron/metabolism/administration &amp; dosage ; Male ; *RNA, Ribosomal, 16S/genetics ; *Powders ; Diarrhea/microbiology ; Feces/microbiology ; Anemia, Iron-Deficiency/microbiology ; },
abstract = {Anemia is highly prevalent globally, especially in young children in low-income countries, where it often overlaps with a high burden of diarrheal disease. Distribution of iron interventions (as supplements or iron-containing multiple micronutrient powders, MNPs) is a key anemia reduction strategy. Small studies in Africa indicate iron may reprofile the gut microbiome towards pathogenic species. We seek to evaluate the safety of iron and MNPs based on their effects on diversity, composition, and function of the gut microbiome in children in rural Bangladesh as part of a large placebo-controlled randomized controlled trial of iron or MNPs given for 3 months (ACTRN12617000660381). In 923 infants, we evaluate the microbiome before, immediately following, and nine months after interventions, using 16S rRNA gene sequencing and shotgun metagenomics in a subset. We identify no increase in diarrhea with either treatment. In our primary analysis, neither iron nor MNPs alter gut microbiome diversity or composition. However, when not adjusting for multiple comparisons, compared to placebo, children receiving iron and MNPs exhibit reductions in commensal species (e.g., Bifidobacterium, Lactobacillus) and increases in potential pathogens, including Clostridium. These increases are most evident in children with baseline iron repletion and are further supported by trend-based statistical analyses.},
}
@article {pmid39366491,
year = {2024},
author = {Chen, G and Zhang, H and Sun, J and Yan, Q and Feng, G},
title = {Municipal-treated wastewater as a practical alternative to conventional rice irrigation: effects on antibiotic resistance genes, virulence factors and human bacterial pathogens in soil, and responses of rice grain quality.},
journal = {Chemosphere},
volume = {},
number = {},
pages = {143458},
doi = {10.1016/j.chemosphere.2024.143458},
pmid = {39366491},
issn = {1879-1298},
abstract = {Reuse of municipal-treated wastewater for agricultural irrigation is becoming increasingly prevalent due to growing demand and decline in freshwater supplies. However, the microbial contamination profile, including antibiotic resistance genes (ARGs), virulence factors (VFs), and human bacterial pathogens (HBPs) in agricultural soil irrigated with municipal-treated wastewater for paddy cultivation, was unknown. Here, metagenomic analysis was applied to provide a systematic insight into the resistome, VFs and HBPs in paddy soils irrigated with municipal-treated wastewater. The obtained results revealed that the residual antibiotics in municipal-treated wastewater has an impact on the antibiotic resistome by increasing both the total number and abundance of ARGs. Furthermore, it was found that sul1 could serve as a potential risk indicator for assessing ARG contamination. VFs, core HBP abundance, and dangerous pathogens remain unaffected by municipal-treated wastewater irrigation for paddy. The good coexistence patterns of ARGs-HBPs and ARGs-VFs demonstrated the presence of resistant pathogenic bacteria. The network analysis revealed that ARGs-bearing Legionella pneumophila, Mycobacterium marinum, Bordetella pertussis, Staphylococcus aureus, and Pseudomonas aeruginosa might be ranked as high-risk HBPs. Additionally, our investigation also demonstrated that reuse of municipal-treated wastewater for agricultural irrigation had no detrimental effects on rice plant growth and grain quality. This study was the first to investigate the response of VFs and HBPs in paddy soil under long-term municipal-treated wastewater irrigation. The obtained results provide a scientific basis for the safe application of municipal-treated wastewater.},
}
@article {pmid39365087,
year = {2024},
author = {Hourdel, V and Balière, C and Vanhomwegen, J and Brisebarre, A and Grassin, Q and Manuguerra, J-C and Kallel, H and Demar, M and Dacheux, L and Caro, V},
title = {Complete genome sequence of a vampire bat-related rabies virus obtained by metagenomics from a patient with encephalitis of unknown etiology, French Guiana.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0051424},
doi = {10.1128/mra.00514-24},
pmid = {39365087},
issn = {2576-098X},
abstract = {We report the complete genome sequence of a rabies virus obtained by direct metagenomics from the cerebellum of a gold panner who died of unknown encephalitis in French Guiana. Phylogenetic analysis exhibited a close genetic relationship with vampire bat-related isolates, confirming the second case of human rabies identified in this territory.},
}
@article {pmid39365058,
year = {2024},
author = {Corbett, GA and Moore, R and Feehily, C and Killeen, SL and O'Brien, E and Van Sinderen, D and Matthews, E and O'Flaherty, R and Rudd, PM and Saldova, R and Walsh, CJ and Lawton, EM and MacIntyre, DA and Corcoran, S and Cotter, PD and McAuliffe, FM},
title = {Dietary amino acids, macronutrients, vaginal birth, and breastfeeding are associated with the vaginal microbiome in early pregnancy.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0113024},
doi = {10.1128/spectrum.01130-24},
pmid = {39365058},
issn = {2165-0497},
abstract = {UNLABELLED: The vaginal microbiome is a key player in the etiology of spontaneous preterm birth. This study aimed to illustrate maternal environmental factors associated with vaginal microbiota composition and function in pregnancy. Women in healthy pregnancy had vaginal microbial sampling from the posterior vaginal fornix performed at 16 weeks gestation. After shotgun metagenomic sequencing, heatmaps of relative abundance data were generated. Community state type (CST) was assigned, and alpha diversity was calculated. Demography, obstetric history, well-being, exercise, and diet using food frequency questionnaires were collected and compared against microbial parameters. A total of 119 pregnant participants had vaginal metagenomic sequencing performed. Factors with strongest association with beta diversity were dietary lysine (adj-R[2] 0.113, P = 0.002), valine (adj-R[2] 0.096, P = 0.004), leucine (adj-R[2] 0.086, P = 0.003), and phenylalanine (adj-R[2] 0.085, P = 0.005, Fig. 2D). Previous vaginal delivery and breastfeeding were associated with vaginal beta diversity (adj-R[2] 0.048, P = 0.003; adj-R[2] 0.045, P = 0.004), accounting for 8.5% of taxonomy variation on redundancy analysis. Dietary fat, starch, and maltose were positively correlated with alpha diversity (fat +0.002 SD/g, P = 0.025; starch +0.002 SD/g, P = 0.043; maltose +0.440 SD/g, P = 0.013), particularly in secretor-positive women. Functional signature was associated with CST, maternal smoking, and dietary phenylalanine, accounting for 8.9%-11% of the variation in vaginal microbiome functional signature. Dietary amino acids, previous vaginal delivery, and breastfeeding history were associated with vaginal beta diversity. Functional signature of the vaginal microbiome differed with community state type, smoking, dietary phenylalanine, and vitamin K. Increased alpha diversity correlated with dietary fat and starch. These data provide a novel snapshot into the associations between maternal environment, nutrition, and the vaginal microbiome.<br><br>IMPORTANCE: This secondary analysis of the MicrobeMom randomized controlled trial reveals that dietary amino acids, macronutrients, previous vaginal birth, and breastfeeding have the strongest associations with vaginal taxonomy in early pregnancy. Function of the vaginal niche is associated mainly by species composition, but smoking, vitamin K, and phenylalanine also play a role. These associations provide an intriguing and novel insight into the association between host factors and diet on the vaginal microbiome in pregnancy and highlight the need for further investigation into the complex interactions between the diet, human gut, and vaginal microbiome.},
}
@article {pmid39365049,
year = {2024},
author = {Won, S and Cho, S and Kim, H},
title = {rRNA operon improves species-level classification of bacteria and microbial community analysis compared to 16S rRNA.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0093124},
doi = {10.1128/spectrum.00931-24},
pmid = {39365049},
issn = {2165-0497},
abstract = {UNLABELLED: Precise identification of species is fundamental in microbial genomics and is crucial for understanding the microbial communities. While the 16S rRNA gene, particularly its V3-V4 regions, has been extensively employed for microbial identification, however has limitations in achieving species-level resolution. Advancements in long-read sequencing technologies have highlighted the rRNA operon as a more accurate marker for microbial classification and analysis than the 16S rRNA gene. This study aims to compare the accuracy of species classification and microbial community analysis using the rRNA operon versus the 16S rRNA gene. We evaluated the species classification accuracy of the rRNA operon,16S rRNA gene, and 16S rRNA V3-V4 regions using a BLAST-based method and a k-mer matching-based method with public data available from NCBI. We further performed simulations to model microbial community analysis. We accessed the performance using each marker in community composition estimation and differential abundance analysis. Our findings demonstrate that the rRNA operon offers an advantage over the 16S rRNA gene and its V3-V4 regions for species-level classification within the genus. When applied to microbial community analysis, the rRNA operon enables a more accurate determination of composition. Using the rRNA operon yielded more reliable results in differential abundance analysis as well.<br><br>IMPORTANCE: We quantitatively demonstrated that the rRNA operon outperformed the 16S rRNA and its V3-V4 regions in accuracy for both individual species identification and species-level microbial community analysis. Our findings can provide guidelines for selecting appropriate markers in the field of microbial research.},
}
@article {pmid39364864,
year = {2024},
author = {Dong, W and Hu, S and Yu, J and Liu, Y and Zeng, S and Duan, X and Deng, Y and Wang, Y and Yin, J and Xing, B and Shu, Z},
title = {Study on the Antidepressant Effect of Zhizichi Decoction by Regulating Metabolism and Intestinal Flora.},
journal = {Combinatorial chemistry &amp; high throughput screening},
volume = {},
number = {},
pages = {},
doi = {10.2174/0113862073312654240918072945},
pmid = {39364864},
issn = {1875-5402},
abstract = {BACKGROUND: The incidence of depression is increasing year by year, and Zhizichi Decoction（ZZCD）has shown significant efficiency in the clinical treatment of mild depression, but its mechanism of action is still unclear. In this research, network pharmacology and metagenomics combined and metabolomics were used as research methods to explain the scientific connotation of the antidepressant effect of ZZCD from the aspects of the overall effect of organisms and microbial structure and function.<br><br>METHODS: The rat model of depression was established by chronic unpredictable mild stress (CUMS), and the improvement of depressive symptoms was evaluated by behavioral and histopathological methods. Network pharmacology predicted possible targets and important pathways of ZZCD. Metabolomics revealed its possible related biological pathways. Metagenomics showed the disturbance of ZZCD on intestinal microbial diversity structure and associated biological functions in depressed rats.<br><br>RESULTS: ZZCD can improve the behavioral performance of CUMS rats, and can significantly regulate the content of 5-HT, NE and other neurotransmitters in serum and brain tissue, and improve the damaged state of neurons in the hippocampus. Network pharmacology predicts that it mainly acts on biological processes such as inflammatory response and oxidative stress response. Metabolomics found that it affected metabolic pathways such as amino acid metabolism and lipid metabolism. The results of metagenomics showed that it significantly regulated the abundance of Firmicutes and Bacteroidetes. The above results predicted that it may affect signaling pathways such as the nervous system, inflammatory diseases and cell processing.<br><br>CONCLUSION: ZZCD may play an antidepressant role by regulating intestinal probiotics, energy metabolism, and inflammation reduction. This provides a scientific basis for the clinical application of ZZCD in traditional Chinese medicine and also makes it an optional alternative for the treatment of depression.},
}
@article {pmid39364122,
year = {2024},
author = {Zhang, S and Yang, S and Zhuang, Y and Yang, D and Gu, X and Wang, Y and Wang, Z and Chen, R and Yan, F},
title = {Lactobacillus acidophilus CICC 6075 attenuates high-fat diet-induced obesity by improving gut microbiota composition and histidine biosynthesis.},
journal = {Bioscience of microbiota, food and health},
volume = {43},
number = {4},
pages = {367-380},
pmid = {39364122},
issn = {2186-6953},
abstract = {This study aimed to investigate the potential anti-obesity efficacy of Lactobacillus acidophilus CICC 6075. The study analyzed fecal metagenomic data from 120 obese and 100 non-obese individuals. C57BL/6 mice on normal diet or high-fat diet (HFD) were treated with L. acidophilus CICC 6075 by daily oral gavage for 12 weeks, followed by evaluations of the obesity phenotype. Metagenomic analysis revealed depletion of L. acidophilus in obese individuals. Administration of L. acidophilus CICC 6075 attenuated excessive weight gain and fat accumulation and maintained the intestinal barrier in HFD-induced obese mice. Sequencing results showed that HFD hindered α- and β-diversity while reducing the relative abundance of Lactobacillus and norank_f_Muribaculaceae and significantly increasing the relative abundance of Ileibacterium. L. acidophilus CICC 6075 reversed these results and reduced the Firmicutes/Bacteroidetes ratio. Supplementation of L. acidophilus CICC 6075 enhanced histidine biosynthesis, inhibited the NF-κB pathway, and significantly reduced the expression levels of inflammatory factors in adipose tissue. These results indicate that L. acidophilus CICC 6075 alleviates HFD-induced obesity in mice by inhibiting the activation of the NF-κB pathway and enhancing gut microbiota functionality. This suggests that L. acidophilus CICC 6075 may be a good candidate probiotic for preventing obesity.},
}
@article {pmid39364006,
year = {2024},
author = {Rasal, KD and Kumar, PV and Risha, S and Asgolkar, P and Harshavarthini, M and Acharya, A and Shinde, S and Dhere, S and Rasal, A and Sonwane, A and Brahmane, M and Sundaray, JK and Nagpure, N},
title = {Genetic improvement and genomic resources of important cyprinid species: status and future perspectives for sustainable production.},
journal = {Frontiers in genetics},
volume = {15},
number = {},
pages = {1398084},
pmid = {39364006},
issn = {1664-8021},
abstract = {Cyprinid species are the most cultured aquatic species around the world in terms of quantity and total value. They account for 25% of global aquaculture production and significantly contribute to fulfilling the demand for fish food. The aquaculture of these species is facing severe concerns in terms of seed quality, rising feed costs, disease outbreaks, introgression of exotic species, environmental impacts, and anthropogenic activities. Numerous researchers have explored biological issues and potential methods to enhance cyprinid aquaculture. Selective breeding is extensively employed in cyprinid species to enhance specific traits like growth and disease resistance. In this context, we have discussed the efforts made to improve important cyprinid aquaculture practices through genetic and genomic approaches. The recent advances in DNA sequencing technologies and genomic tools have revolutionized the understanding of biological research. The generation of a complete genome and other genomic resources in cyprinid species has significantly strengthened molecular-level investigations into disease resistance, growth, reproduction, and adaptation to changing environments. We conducted a comprehensive review of genomic research in important cyprinid species, encompassing genome, transcriptome, proteome, metagenome, epigenome, etc. This review reveals that considerable data has been generated for cyprinid species. However, the seamless integration of this valuable data into genetic selection programs has yet to be achieved. In the upcoming years, genomic techniques, gene transfer, genome editing tools are expected to bring a paradigm shift in sustainable cyprinid aquaculture production. The comprehensive information presented here will offer insights for the cyprinid aquaculture research community.},
}
@article {pmid39363816,
year = {2024},
author = {Sarker, S and Klukowski, N and Talukder, S and Gupta, SD and Vaughan-Higgins, R},
title = {Evidence of a highly divergent novel parvovirus in Australia's critically endangered western ground parrot/kyloring (Pezoporus flaviventris).},
journal = {Australian veterinary journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/avj.13378},
pmid = {39363816},
issn = {1751-0813},
abstract = {Detecting pathogens in endangered animal populations is vital for understanding and mitigating threats to their survival. The critically endangered western ground parrot (Pezoporus flaviventris, WGP), with a population as low as 150 individuals in Australia, faces an imminent risk of extinction. Despite this urgency, research on viral pathogens in this species remains limited. This study aimed to identify and characterise viruses present in faecal samples from seven individual WGP using a viral metagenomic approach. Analysis of the sequenced datasets revealed the presence of a novel virus belonging to the Parvoviridae family, named psittaciform chaphamaparvovirus 7 (PsChPV-7). The genome of PsChPV-7 contains typical structural and functional gene sequences found in Parvoviridae but is highly divergent, indicating its classification as a distinct species. Phylogenetic analysis placed PsChPV-7 within a unique sub-clade of the Chaphamaparvovirus genus, suggesting its evolutionary significance as an ancient lineage within this group. These findings may contribute to the development of strategic management and biosecurity plans aimed at conserving this endangered WGP.},
}
@article {pmid39363670,
year = {2024},
author = {Wang, R and Tang, G and Lu, Y and Zhang, D and Cai, S and He, H and Zhang, H and Xiong, Q},
title = {Root physiological and soil microbial mechanisms underlying responses to nitrogen deficiency and compensation in Indica and Japonica rice.},
journal = {Physiologia plantarum},
volume = {176},
number = {5},
pages = {e14549},
doi = {10.1111/ppl.14549},
pmid = {39363670},
issn = {1399-3054},
support = {2021KY47//Jiangxi Province Postdoctoral Scientific Research Funding/ ; PAPD//Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; 32101816//National Natural Science Foundation of China/ ; SJCX23_1974//Postgraduate Research &amp; Practice Innovation Program of Jiangsu Province/ ; 2021M702768//project funded by the China Postdoctoral Science Foundation/ ; 2021K292B//Jiangsu Province Postdoctoral Research Funding/ ; },
mesh = {*Oryza/microbiology/metabolism/genetics/physiology ; *Nitrogen/metabolism ; *Plant Roots/microbiology/metabolism ; *Soil Microbiology ; *Rhizosphere ; Fertilizers ; Bacteria/metabolism/genetics/classification ; },
abstract = {Compensatory effects are common biological phenomena in nature. In this study, we investigated the changes in root nitrogen uptake, root morphological and physiological responses, and changes in the rhizosphere soil microbial communities of indica and japonica rice during a nitrogen deficiency-sensitive period and an effective compensation period with double the nitrogen supply. We conducted a bucket experiment using Suxiu 867 (a japonica rice variety) and Yangxian You 918 (an indica rice variety). Treatments included CK (constant distribution of nitrogen fertilizer at each growth stage, represented by CK867 and CK918) and NDC (nitrogen deficiency in the tillering stage, double nitrogen application in the ear differentiation stage to compensate, represented by NDC867 and NDC918) variations. Both varieties presented the highest δ[15]N and [15]N abundances and Ndff (refers to the proportion of nitrogen in a plant's body that comes directly from the fertilizer applied.) in rice under the NDC treatment. Metagenomic sequencing of rhizospheric soil showed that the dominant bacterial groups at the phylum level among each treatment were Actinobacteria, Proteobacteria, Chloroflexi, Acidobacteria, Gemmatimonadetes, and Nitrospirae. The rhizosphere of indica rice was more enriched with the microbial communities involved in nitrogen metabolism, which contributed to higher nitrogen utilization efficiency. A correlation-based network was constructed and provides insights into the formation of nitrogen deficiency compensation effects and contributes to the enhancement of nitrogen uptake and utilization efficiency in rice production.},
}
@article {pmid39363651,
year = {2024},
author = {Vazquez Bucheli, JE and Lee, Y and Kim, B and Azevedo, NF and Azevedo, AS and Todorov, SD and Ji, Y and Kang, H and Holzapfel, WH},
title = {Use of FISH-FLOW as a Method for the Identification and Quantification of Bacterial Populations.},
journal = {Molecular nutrition &amp; food research},
volume = {},
number = {},
pages = {e2400494},
doi = {10.1002/mnfr.202400494},
pmid = {39363651},
issn = {1613-4133},
support = {NRF-2018M3A9F3021964//NRF Korea/ ; RS-2023-00222687//NRF Korea/ ; 739489//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; 2023/05394-9//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; LA/P/0045/2020UIDP/00511/2020,POCI-01-0145-FEDER-030431//FCT Portugal/ ; },
abstract = {The gastrointestinal tract (GIT) harbors the largest group of microbiotas among the microbial communities of the human host. The resident organisms typical of a healthy gut are well adapted to the gastrointestinal environment while alteration of these populations can trigger disorders that may affect the health and well-being of the host. Various investigations have applied different tools to study bacterial communities in the gut and their correlation with gastrointestinal disorders such as inflammatory bowel disease (IBD), obesity, and diabetes. This study proposes fluorescent in situ hybridization, combined with flow cytometry (FISH-FLOW), as an alternative approach for phylum level identification of Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria and quantification of target bacteria from the GIT based on analysis of fecal samples, where results are validated by quantitative polymerase chain reaction (qPCR) and 16S ribosomal ribonucleic acid (16s rRNA) sequencing. The results obtained via FISH-FLOW experimental approach show high specificity for the developed probes for hybridization with the target bacteria. The study, therefore, suggests the FISH-FLOW as a reliable method for studying bacterial communities in the gut with results correlating well with those of metagenomic investigations of the same fecal samples.},
}
@article {pmid39363203,
year = {2024},
author = {Viana, PAB and Tschoeke, DA and de Moraes, L and Santos, LA and Barral-Netto, M and Khouri, R and Ramos, PIP and Meirelles, PM},
title = {Design and implementation of a metagenomic analytical pipeline for respiratory pathogen detection.},
journal = {BMC research notes},
volume = {17},
number = {1},
pages = {291},
pmid = {39363203},
issn = {1756-0500},
support = {2023-PPI-007//Rockefeller Foundation/ ; },
abstract = {OBJECTIVE: We developed an in-house bioinformatics pipeline to improve the detection of respiratory pathogens in metagenomic sequencing data. This pipeline addresses the need for short-time analysis, high accuracy, scalability, and reproducibility in a high-performance computing environment.<br><br>RESULTS: We evaluated our pipeline using ninety synthetic metagenomes designed to simulate nasopharyngeal swab samples. The pipeline successfully identified 177 out of 204 respiratory pathogens present in the compositions, with an average processing time of approximately 4&#xa0;min per sample (processing 1&#xa0;million paired-end reads of 150 base pairs). For the estimation of all the 470 taxa included in the compositions, the pipeline demonstrated high accuracy, identifying 420 and achieving a correlation of 0.9 between their actual and predicted relative abundances. Among the identified taxa, 27 were significantly underestimated or overestimated, including only three clinically relevant pathogens. We also validated the pipeline by applying it to a clinical dataset from a study on metagenomic pathogen characterization in patients with acute respiratory infections and successfully identified all pathogens responsible for the diagnosed infections. These findings underscore the pipeline's effectiveness in pathogen detection and highlight its potential utility in respiratory pathogen surveillance.},
}
@article {pmid39363100,
year = {2024},
author = {Chu, VT and Glascock, A and Donnell, D and Grabow, C and Brown, CE and Ward, R and Love, C and Kalantar, KL and Cohen, SE and Cannon, C and Woodworth, MH and Kelley, CF and Celum, C and Luetkemeyer, AF and Langelier, CR},
title = {Impact of doxycycline post-exposure prophylaxis for sexually transmitted infections on the gut microbiome and antimicrobial resistome.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
pmid = {39363100},
issn = {1546-170X},
abstract = {Doxycycline post-exposure prophylaxis (doxy-PEP) reduces bacterial sexually transmitted infections among men who have sex with men and transgender women. Although poised for widespread clinical implementation, the impact of doxy-PEP on antimicrobial resistance remains a primary concern as its effects on the gut microbiome and resistome, or the antimicrobial resistance genes (ARGs) present in the gut microbiome, are unknown. To investigate these effects, we studied participants from the DoxyPEP trial, a randomized clinical trial comparing doxy-PEP use, a one-time doxycycline 200-mg dose taken after condomless sex (DP arm, n = 100), to standard of care (SOC arm, n = 50) among men who have sex with men and transgender women. From self-collected rectal swabs at enrollment (day-0) and after 6 months (month-6), we performed metagenomic DNA sequencing (DNA-seq) or metatranscriptomic RNA sequencing (RNA-seq). DNA-seq data were analyzable from 127 samples derived from 89 participants, and RNA-seq data were analyzable from 86 samples derived from 70 participants. We compared the bacterial microbiome and resistome between the two study arms and over time. The median number of doxycycline doses taken since enrollment by participants with DNA-seq data was zero (interquartile range (IQR): 0-7 doses) for the SOC arm and 42 (IQR: 27-64 doses) for the DP arm. Tetracycline ARGs were detected in all day-0 DNA-seq samples and in 85% of day-0 RNA-seq samples. The proportional mass of tetracycline ARGs in the resistome increased between day-0 and month-6 in DP participants from 46% to 51% in the metagenome (P = 2.3 × 10[-2]) and from 4% to 15% in the metatranscriptome (P = 4.5 × 10[-6]), but no statistically significant increases in other ARG classes were observed. Exposure to a higher number of doxycycline doses correlated with proportional enrichment of tetracycline ARGs in the metagenome (Spearman's ρ = 0.23, P = 9.0 × 10[-3]) and metatranscriptome (Spearman's ρ = 0.55, P = 3.7 × 10[-8]). Bacterial microbiome alpha diversity, beta diversity and total bacterial mass did not differ between day-0 and month-6 samples from DP participants when assessed by either DNA-seq or RNA-seq. In an abundance-based correlation analysis, we observed an increase over time in the strength of the correlation between tetracycline ARGs and specific bacterial taxa, including some common human pathogens. In sum, doxy-PEP use over a 6-month period was associated with an increase in the proportion of tetracycline ARGs comprising the gut resistome and an increase in the expression of tetracycline ARGs. At 6 months of doxy-PEP use, no residual differences were observed in alpha and beta diversity or taxonomic composition of the gut microbiome. As doxy-PEP is implemented as a public health strategy, further studies and population-level surveillance of doxycycline-resistant pathogens are needed to understand the implications of these findings. ClinicalTrials.gov registration number: NCT03980223 .},
}
@article {pmid39362974,
year = {2024},
author = {Khan, NA and Majumder, A and Singh, S and Ramamurthy, PC and Prakash, SK and Farooqi, IH and Mozaffari, N and Lawal, DU and Aljundi, IH},
title = {C/N ratio effect on oily wastewater treatment using column type SBR: machine learning prediction and metagenomics study.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {22950},
pmid = {39362974},
issn = {2045-2322},
mesh = {*Wastewater/chemistry ; *Nitrogen/metabolism ; *Carbon/metabolism ; *Machine Learning ; *Metagenomics/methods ; Bioreactors/microbiology ; Water Purification/methods ; Phosphorus/metabolism/analysis ; Waste Disposal, Fluid/methods ; },
abstract = {The sequencing batch reactor has emerged as a promising technology in treating wastewater; however, its application in the treatment of generated water still needs to be explored. This research gap led to the investigation of various carbon-to-nitrogen (C/N) ratios in a column-type sequencing batch reactor (cSBR). The resulting data and model demonstrated that augmenting the SND process with an external carbon source is effective until the C/N ratio reaches 15, ultimately eliminating nitrogen in the produced water. Conversely, a reduced C/N ratio can limit the ability of polyphosphate-accumulating organisms to incorporate carbon into polyphosphate synthesis, thereby decreasing phosphorus removal efficiency within the cSBR. When the C/N ratio ranged from 6 to 8, and the mixed liquor suspended solids concentration was high, the average phosphate removal was approximately 55%, compared to only around 25% when the C/N ratio was less than 6.},
}
@article {pmid39362665,
year = {2024},
author = {Tiew, PY and Leung, JM and Mac Aogáin, M and Johal, P and Jaggi, TK and Yuen, ACY and Ivan, FX and Yang, J and Afshar, T and Tee, A and Koh, MS and Lim, YH and Wong, A and Chandrasekaran, L and Dacanay, JG and Drautz-Moses, DI and Ong, TH and Abisheganaden, JA and Chew, FT and Schuster, SC and Carlsten, C and Chotirmall, SH},
title = {Residential exposure to Aspergillus spp. is associated with exacerbations in COPD.},
journal = {The European respiratory journal},
volume = {},
number = {},
pages = {},
doi = {10.1183/13993003.00907-2024},
pmid = {39362665},
issn = {1399-3003},
abstract = {BACKGROUND: Sensitisation to Aspergillus fumigatus is linked to worse outcomes in patients with chronic obstructive pulmonary disease (COPD), however, its prevalence and clinical implications in domestic (residential) settings remains unknown.<br><br>METHODS: Individuals with COPD (n=43) recruited in Singapore had their residences prospectively sampled and assessed by shotgun metagenomic sequencing including indoor air, outdoor air, and touch surfaces (total: 126 specimens). The abundance of environmental A. fumigatus and the occurrence of A. fumigatus (Asp f) allergens in the environment were determined and immunological responses to A. fumigatus allergens determined in association with clinical outcomes including exacerbation frequency. Findings were validated in 12 individuals (31 specimens) with COPD in Vancouver, Canada, a climatically different region.<br><br>RESULTS: 157 metagenomes from 43 homes were assessed. Eleven and nine separate Aspergillus spp. were identified in Singapore and Vancouver respectively. Despite climatic, temperature, and humidity variation, A. fumigatus was detectable in the environment from both locations. The relative abundance of environmental A. fumigatus was significantly associated with exacerbation frequency in both Singapore (r=0.27, p=0.003) and Vancouver (r=0.49, p=0.01) and individuals with higher Asp f 3 sensitisation responses lived in homes with a greater abundance of environmental Asp f 3 allergens (p=0.037). Patients exposed and sensitised to Asp f 3 allergens demonstrated a higher rate of COPD exacerbations at 1-year follow-up (p=0.021).<br><br>CONCLUSION: Environmental A. fumigatus exposure in the home environment including air and surfaces with resulting sensitisation carries pathogenic potential in individuals with COPD. Targeting domestic A. fumigatus abundance may reduce COPD exacerbations.},
}
@article {pmid39362131,
year = {2024},
author = {Yang, T and Wang, X and Ng, HY and Huang, S and Zheng, X and Bi, X},
title = {Airborne antibiotic resistome from sludge dewatering systems: Mobility, pathogen accessibility, cross-media migration propensity, impacting factors, and risks.},
journal = {Water research},
volume = {267},
number = {},
pages = {122552},
doi = {10.1016/j.watres.2024.122552},
pmid = {39362131},
issn = {1879-2448},
abstract = {Bioaerosol contamination was considered as a potential health threat in sludge dewatering systems (SDSs), while emission and risk of airborne antibiotic resistome remain largely unclear. Herein, seasonal investigations of fine particulate matter (PM2.5) were conducted using metagenomics-based methods within and around different SDSs, together with an analysis of sewage sludge. Featured with evident seasonality, antibiotic resistance genes (ARGs) in SDS-PM2.5 also possessed greater accumulation, transfer, and pathogen accessibility than those in ambient air PM2.5. Mobile ARGs in SDS-PM2.5 mainly encoded resistance to tetracycline, and most were flanked by integrase. Some pathogenic antibiotic resistant bacteria (PARB), including Enterobacter asburiae, Escherichia coli, Enterococcus faecium, and Staphylococcus aureus, also carried mobile genetic elements in SDS-PM2.5. Dewatering behavior actuated > 50.56% of ARG subtypes and > 42.86% of PARB in sewage sludge to aerosolize into air. Relative humidity, temperature, and PM2.5 concentration collectively drove the evolution of bacterial community and indirectly promoted the antibiotic resistance of SDS-PM2.5. SDS-PM2.5 posed more serious resistome risks than sewage sludge and ambient air PM2.5, and the highest levels were discovered in winter. These findings underline the role of dewatering behavior in facilitating resistome's aerosolization, and the need to mitigate this potential air pollution.},
}
@article {pmid39362120,
year = {2024},
author = {Gao, S and Li, S and Cao, S and Zhong, H and He, Z},
title = {Disclosing the key role of Fe/As/Cu in community co-occurrence and microbial recruitment in metallurgical ruins.},
journal = {Journal of hazardous materials},
volume = {480},
number = {},
pages = {135889},
doi = {10.1016/j.jhazmat.2024.135889},
pmid = {39362120},
issn = {1873-3336},
abstract = {Mining activities have led to the persistent presence of substantial heavy metals at metallurgical sites. However, the impact of long-term and complex heavy metal pollution in metallurgical ruins on the structure and spatial shift of microbiome remains unclear. In this study, we focused on various types of metallurgical sites to uncover the occurrence of heavy metals in abandoned mines and the response patterns of microbial communities. The results indicate that mining activities have caused severe exceedances of multiple heavy metals, with AsBio, CuBio, and FeBio being the primary factors affecting community structure and function. Co-occurrence network analyses suggest that several genera, including Ellin6515, Cupriavidus, Acidobacteria genus RB41, Vicinamibacteraceae, Blastococcus, and Sphingomonas, may play significant roles in the synergistic metabolism of communities responding to Fe-Cu-As stress. Although random dispersal contributed to community migration, null models emphasized that variable selection predominates in the spatial turnover of community composition. Additionally, metagenomic prediction (PICRUSt2) identified key genes involved in stress and detoxification strategies of heavy metals. The composite heavy metal stress strengthened the relationship between network structure and the potential function of the community, along with critical ecosystem functions. Our findings demonstrated that microbial interactions were crucial for ecosystem management and the ecological consequences of heavy metal pollution remediation.},
}
@article {pmid39361891,
year = {2024},
author = {Ramos-Barbero, MD and Gómez-Gómez, C and Vique, G and Sala-Comorera, L and Rodríguez-Rubio, L and Muniesa, M},
title = {Recruitment of complete crAss-like phage genomes reveals their presence in chicken viromes, few human-specific phages, and lack of universal detection.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae192},
pmid = {39361891},
issn = {1751-7370},
abstract = {The order Crassvirales, which includes the prototypical crAssphage (p-crAssphage), is predominantly associated with humans, rendering it the most abundant and widely distributed group of DNA phages in the human gut. The reported human specificity and wide global distribution of p-crAssphage makes it a promising human fecal marker. However, the specificity for the human gut as well as the geographical distribution around the globe of other members of the order Crassvirales remains unknown. To determine this, a recruitment analysis using 91 complete, non-redundant genomes of crAss-like phages in human and animal viromes revealed that only 13 crAss-like phages among the 91 phages analyzed were highly specific to humans, and p-crAssphage was not in this group. Investigations to elucidate whether any characteristic of the phages was responsible for their prevalence in humans showed that the 13 human crAss-like phages do not share a core genome. Phylogenomic analysis placed them in three independent families, indicating that within the Crassvirales group, human specificity is likely not a feature of a common ancestor but rather was introduced on separate/independent occasions in their evolutionary history. The 13 human crAss-like phages showed variable geographical distribution across human metagenomes worldwide, with some being more prevalent in certain countries than in others, but none being universally identified. The varied geographical distribution and the absence of a phylogenetic relationship among the human crAss-like phages are attributed to the emergence and dissemination of their bacterial host, the symbiotic human strains of Bacteroides, across various human populations occupying diverse ecological niches worldwide.},
}
@article {pmid39360992,
year = {2024},
author = {Mayne, R and Secret, S and Geoghegan, C and Trebes, A and Kean, K and Reid, K and Lin, GL and Ansari, MA and de Cesare, M and Bonsall, D and Elliott, I and Piazza, P and Brown, A and Bray, J and Knight, JC and Harvala, H and Breuer, J and Simmonds, P and Bowden, RJ and Golubchik, T},
title = {Castanet: A pipeline for rapid analysis of targeted multi-pathogen genomic data.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btae591},
pmid = {39360992},
issn = {1367-4811},
abstract = {MOTIVATION: Target enrichment strategies generate genomic data from multiple pathogens in a single process, greatly improving sensitivity over metagenomic sequencing and enabling cost-effective, high throughput surveillance and clinical applications. However, uptake by research and clinical laboratories is constrained by an absence of computational tools that are specifically designed for the analysis of multi-pathogen enrichment sequence data. Here we present an analysis pipeline, Castanet, for use with multi-pathogen enrichment sequencing data. Castanet is designed to work with short-read data produced by existing targeted enrichment strategies, but can be readily deployed on any BAM file generated by another methodology. Also included are an optional graphical interface and installer script.<br><br>RESULTS: In addition to genome reconstruction, Castanet reports method-specific metrics that enable quantification of capture efficiency, estimation of pathogen load, differentiation of low-level positives from contamination, and assessment of sequencing quality. Castanet can be used as a traditional end-to-end pipeline for consensus generation, but its strength lies in the ability to process a flexible, pre-defined set of pathogens of interest directly from multi-pathogen enrichment experiments. In our tests, Castanet consensus sequences were accurate reconstructions of reference sequences, including in instances where multiple strains of the same pathogen were present. Castanet performs effectively on standard computers and can process the entire output of a 96-sample enrichment sequencing run (50M reads) using a single batch process command, in $<$2&#x2009;h.<br><br>Source code freely available under GPL-3 license at https://github.com/MultipathogenGenomics/castanet, implemented in Python 3.10 and supported in Ubuntu Linux 22.04.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data available at the journal's web site. Supporting sequencing data available at https://www.ebi.ac.uk/ena/browser/view/PRJEB77004.},
}
@article {pmid39360442,
year = {2024},
author = {Guo, N and Gui, YJ and Chen, Y},
title = {Vitrectomy Combined with Repeated Intravitreal Injection of Ceftazidime for the Treatment of Brucellosis Endophthalmitis: A Case Report and Literature Review.},
journal = {Seminars in ophthalmology},
volume = {},
number = {},
pages = {1-4},
doi = {10.1080/08820538.2024.2412050},
pmid = {39360442},
issn = {1744-5205},
abstract = {PURPOSE: To present a treatment regimen for Brucellosis endophthalmitis that resulted in a good visual outcome. Additionally, we conducted a literature review on the treatment and visual prognosis of related cases.<br><br>CASE PRESENTATION: A 49-year-old woman with the chief complaint of decreased vision and redness in the right eye was initially diagnosed with noninfectious uveitis and prescribed high-dose steroids which led to transient improvement followed by a decline in vision. An infectious cause was suspected. Metagenomic next-generation sequencing of vitreous fluid and serological testing confirmed Brucella melitensis infection. The patient underwent vitrectomy combined with six intravitreal injections of ceftazidime in the right eye in addition to systemic antibiotic treatment. The intraocular inflammation was completely resolved, and the visual acuity recovered to 20/25, which is the best-documented recovery in Brucella endophthalmitis cases, as revealed by the literature review.<br><br>CONCLUSION: Vitrectomy combined with repeated intravitreal injections of ceftazidime can enhance the treatment for brucellosis endophthalmitis and achieve a better visual prognosis.},
}
@article {pmid39360247,
year = {2024},
author = {Yepes-García, J and Falquet, L},
title = {Metagenome quality metrics and taxonomical annotation visualization through the integration of MAGFlow and BIgMAG.},
journal = {F1000Research},
volume = {13},
number = {},
pages = {640},
pmid = {39360247},
issn = {2046-1402},
mesh = {*Metagenome ; *Software ; Metagenomics/methods ; Molecular Sequence Annotation/methods ; },
abstract = {BACKGROUND: Building Metagenome-Assembled Genomes (MAGs) from highly complex metagenomics datasets encompasses a series of steps covering from cleaning the sequences, assembling them to finally group them into bins. Along the process, multiple tools aimed to assess the quality and integrity of each MAG are implemented. Nonetheless, even when incorporated within end-to-end pipelines, the outputs of these pieces of software must be visualized and analyzed manually lacking integration in a complete framework.<br><br>METHODS: We developed a Nextflow pipeline (MAGFlow) for estimating the quality of MAGs through a wide variety of approaches (BUSCO, CheckM2, GUNC and QUAST), as well as for annotating taxonomically the metagenomes using GTDB-Tk2. MAGFlow is coupled to a Python-Dash application (BIgMAG) that displays the concatenated outcomes from the tools included by MAGFlow, highlighting the most important metrics in a single interactive environment along with a comparison/clustering of the input data.<br><br>RESULTS: By using MAGFlow/BIgMAG, the user will be able to benchmark the MAGs obtained through different workflows or establish the quality of the MAGs belonging to different samples following the divide and rule methodology.<br><br>CONCLUSIONS: MAGFlow/BIgMAG represents a unique tool that integrates state-of-the-art tools to study different quality metrics and extract visually as much information as possible from a wide range of genome features.},
}
@article {pmid39359923,
year = {2024},
author = {Shi, Z and Zhu, X and Gao, W and Yu, S and Zhan, L},
title = {Extracorporeal membrane oxygenation in acute respiratory distress syndrome caused by elderly tuberculous meningitis: a case report and review of the literature.},
journal = {Frontiers in medicine},
volume = {11},
number = {},
pages = {1457413},
pmid = {39359923},
issn = {2296-858X},
abstract = {Diagnosing and clinical management of tuberculous meningitis (TBM) are still challenging for clinicians. Analysis of cerebrospinal fluid (CSF) is an important diagnostic tool for patients with suspected central nervous system (CNS) diseases. Acute respiratory distress syndrome (ARDS), an inflammatory lung injury, can be treated by mechanical ventilation, fluid management, and even extracorporeal membrane oxygenation (ECMO). In addition, metagenomic next-generation sequencing (mNGS) can facilitate the detection of atypical, rare pathogens in clinical specimens. We report a case of a 65-year-old man with ARDS caused by TBM. He was admitted with a fever and shaking. Despite aggressive initial treatment, the patient progressed rapidly and developed ARDS. Without positive results of mNGS and culture, anti-tuberculosis (TB) treatment was started. In order to improve oxygenation levels, he was placed on veno-venous ECMO for 8 days. On day 47, the tracheotomy catheter was pulled out and sealed. The patient was conscious and could communicate with family members as normal.},
}
@article {pmid39359902,
year = {2024},
author = {Haley, E and Luke, N},
title = {From Awareness to Action: Pioneering Solutions for Women's UTI Challenges in the Era of Precision Medicine.},
journal = {International journal of women's health},
volume = {16},
number = {},
pages = {1595-1605},
pmid = {39359902},
issn = {1179-1411},
abstract = {This article aims to bring clinicians' awareness to the widespread impact of urinary tract infection (UTI) on the lives of women and to the advances that offer hope for future improvements in the diagnosis and management of UTI. Thanks to physiological, anatomical, and lifestyle factor differences, women face heightened vulnerability to UTIs compared to men. In fact, women are four times more likely than men to develop a UTI and around half of these women encounter UTI recurrence, which is a significant source of both physical and psychosocial burdens. Despite the current shortcomings in diagnosis and management, emerging diagnostic technologies promise to identify UTIs more accurately and rapidly, offering women hope for a revolution in UTI management. Meanwhile, clinicians have the opportunity to reduce the psychosocial burden by recognizing the value of patients' lived experiences and ensuring their care plan is in alignment with their patients' goals and expectations for medical care.},
}
@article {pmid39359838,
year = {2024},
author = {Obeagu, EI and Okoroiwu, GIA and Ubosi, NI and Obeagu, GU and Onohuean, H and Muhammad, T and Adias, TC},
title = {Revolution in malaria detection: unveiling current breakthroughs and tomorrow's possibilities in biomarker innovation.},
journal = {Annals of medicine and surgery (2012)},
volume = {86},
number = {10},
pages = {5859-5876},
pmid = {39359838},
issn = {2049-0801},
abstract = {The ongoing battle against malaria has seen significant advancements in diagnostic methodologies, particularly through the discovery and application of novel biomarkers. Traditional diagnostic techniques, such as microscopy and rapid diagnostic tests, have their limitations in terms of sensitivity, specificity, and the ability to detect low-level infections. Recent breakthroughs in biomarker research promise to overcome these challenges, providing more accurate, rapid, and non-invasive detection methods. These advancements are critical in enhancing early detection, guiding effective treatment, and ultimately reducing the global malaria burden. Innovative approaches in biomarker detection are leveraging cutting-edge technologies like next-generation sequencing, proteomics, and metabolomics. These techniques have led to the identification of new biomarkers that can be detected in blood, saliva, or urine, offering less invasive and more scalable options for widespread screening. For instance, the discovery of specific volatile organic compounds in the breath of infected individuals presents a revolutionary non-invasive diagnostic tool. Additionally, the integration of machine learning algorithms with biomarker data is enhancing the precision and predictive power of malaria diagnostics, making it possible to distinguish between different stages of infection and identify drug-resistant strains. Looking ahead, the future of malaria detection lies in the continued exploration of multi-biomarker panels and the development of portable, point-of-care diagnostic devices. The incorporation of smartphone-based technologies and wearable biosensors promises to bring real-time monitoring and remote diagnostics to even the most resource-limited settings.},
}
@article {pmid39359390,
year = {2024},
author = {Karamendin, K and Goodman, SJ and Kasymbekov, Y and Kumar, M and Nuralibekov, S and Kydyrmanov, A},
title = {Viral metagenomic survey of Caspian seals.},
journal = {Frontiers in veterinary science},
volume = {11},
number = {},
pages = {1461135},
pmid = {39359390},
issn = {2297-1769},
abstract = {INTRODUCTION: Viral diseases of pinnipeds cause substantial mortality and morbidity and can influence population demography. Viral metagenomic studies can therefore play an important role in pinniped health assessments and disease surveillance relevant to both individual species and in a "One Health" context.<br><br>METHODS: This study used a metagenomic approach with high throughput sequencing to make the first assessment of viral diversity in Caspian seals (Pusa caspica), the only marine mammal species endemic to the Caspian Sea.<br><br>RESULTS: Sequencing libraries from 35 seals sampled 2009-2020 were analysed, finding sequences from the viral families Circoviridae, Parvoviridae, Herpesviridae, Papillomaviridae, Picornaviridae, Caliciviridae, Cruciviridae, Anelloviridae, Smacoviridae, and Orthomyxoviridae, with additional detection of Adenoviridae via PCR. The similarity of viral contigs from Caspian seal to sequences recovered from other pinnipeds ranged from 63.74% (San Miguel sea lion calicivirus) to 78.79% (Seal anellovirus 4).<br><br>DISCUSSION: Some findings represent novel viral species, but overall, the viral repertoire of Caspian seals is similar to available viromes from other pinnipeds. Among the sequences recovered were partial contigs for influenza B, representing only the second such molecular identification in marine mammals. This work provides a foundation for further studies of viral communities in Caspian seals, the diversity of viromes in pinnipeds more generally, and contributes data relevant for disease risk assessments in marine mammals.},
}
@article {pmid39359379,
year = {2024},
author = {Gao, X and Liu, J and Zhang, X and Zhao, T},
title = {Complete mitochondrial genome and phylogenetic analysis of Chloris chloris (Passeriformes: Fringillidae).},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {9},
number = {10},
pages = {1327-1330},
pmid = {39359379},
issn = {2380-2359},
abstract = {In this study, we employed high-throughput metagenomic data to assemble the mitochondrial genome (mitogenome) of the European greenfinch (Chloris chloris; Linnaeus 1758). The circular mitogenome was 16,813 base pairs (bp) in length, containing 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, and 1 control region. The base composition of the mitogenome is 30.6% A, 30.7% C, 14.2% G, and 24.5% T, resulting in a GC content of 44.9%. Phylogenetic analysis, utilizing the concatenation of the 13 mitochondrial PCGs from 32 related species of the order Passeriformes, indicated a closer relationship between C. chloris and C. sinica. Moreover, the genus Chloris was closely related to the genera of Serinus, Crithagra, Carduelis, and Acanthis. This mitogenomic data of C. chloris not only be helpful for species identification but also facilitates our understanding of the evolutionary relationship among different species in genus Chloris, which experienced rapid radiation evolution.},
}
@article {pmid39353343,
year = {2024},
author = {Zheng, X and Li, J and Ouyang, Y and Wu, G and He, X and Wang, D and Zhang, XX},
title = {Ecological linkages between top-down designed benzothiazole-degrading consortia and selection strength: From performance to community structure and functional genes.},
journal = {Water research},
volume = {267},
number = {},
pages = {122491},
doi = {10.1016/j.watres.2024.122491},
pmid = {39353343},
issn = {1879-2448},
abstract = {The inefficient biodegradation and incomplete mineralization of nitrogenous heterocyclic compounds (NHCs) have emerged as a pressing environmental concern. The top-down design offers potential solutions to this issue by targeting improvements in community function, but the ecological linkages between selection strength and the structure and function of desired microbiomes remain elusive. Herein, the integration of metagenomics, culture-based approach, non-targeted metabolite screening and enzymatic verification experiments revealed the effect of enrichment concentration on the top-down designed benzothiazole (BTH, a typical NHC)-degrading consortia. Significant differences were observed for the degradation efficiency and community structure under varying BTH selections. Notably, the enriched consortia at high concentrations of BTH were dominated by genus Rhodococcus, possessing higher degradation rates. Moreover, the isolate Rhodococcus pyridinivorans Rho48 displayed excellent efficiencies in BTH removal (98 %) and mineralization (∼ 60 %) through the hydroxylation and cleavage of thiazole and benzene rings, where cytochrome P450 enzyme was firstly reported to participate in BTH conversion. The functional annotation of 460 recovered genomes from the enriched consortia revealed diverse interspecific cooperation patterns that accounted for the BTH mineralization, particularly Nakamurella and Micropruina under low selection strength, and Rhodococcus and Marmoricola under high selection strength. This study highlights the significance of selection strength in top-down design of synthetic microbiomes for degrading refractory organic pollutants, providing valuable guidance for designing functionally optimized microbiomes used in environmental engineering.},
}
@article {pmid39358810,
year = {2024},
author = {Meng, L and Jin, H and Yulug, B and Altay, O and Li, X and Hanoglu, L and Cankaya, S and Coskun, E and Idil, E and Nogaylar, R and Ozsimsek, A and Shoaie, S and Turkez, H and Nielsen, J and Zhang, C and Borén, J and Uhlén, M and Mardinoglu, A},
title = {Multi-omics analysis reveals the key factors involved in the severity of the Alzheimer's disease.},
journal = {Alzheimer's research &amp; therapy},
volume = {16},
number = {1},
pages = {213},
pmid = {39358810},
issn = {1758-9193},
abstract = {Alzheimer's disease (AD) is a debilitating neurodegenerative disorder with a global impact, yet its pathogenesis remains poorly understood. While age, metabolic abnormalities, and accumulation of neurotoxic substances are potential risk factors for AD, their effects are confounded by other factors. To address this challenge, we first utilized multi-omics data from 87 well phenotyped AD patients and generated plasma proteomics and metabolomics data, as well as gut and saliva metagenomics data to investigate the molecular-level alterations accounting the host-microbiome interactions. Second, we analyzed individual omics data and identified the key parameters involved in the severity of the dementia in AD patients. Next, we employed Artificial Intelligence (AI) based models to predict AD severity based on the significantly altered features identified in each omics analysis. Based on our integrative analysis, we found the clinical relevance of plasma proteins, including SKAP1 and NEFL, plasma metabolites including homovanillate and glutamate, and Paraprevotella clara in gut microbiome in predicting the AD severity. Finally, we validated the predictive power of our AI based models by generating additional multi-omics data from the same group of AD patients by following up for 3 months. Hence, we observed that these results may have important implications for the development of potential diagnostic and therapeutic approaches for AD patients.},
}
@article {pmid39358791,
year = {2024},
author = {Wirajana, IN and Ariantari, NP and Shyu, DJH and Vaghamshi, N and Antaliya, K and Dudhagara, P},
title = {Prokaryotic communities profiling of Indonesian hot springs using long-read Oxford Nanopore sequencing.},
journal = {BMC research notes},
volume = {17},
number = {1},
pages = {286},
pmid = {39358791},
issn = {1756-0500},
support = {B/530-4/UN14.4A/PT.01.03/2023//Udayana University International Senior Fellowship (UNISERF) grant for year 2023 (Grant Number: B/530-4/UN14.4A/PT.01.03/2023), Udayana University, Bali, Indonesia/ ; },
abstract = {OBJECTIVES: Indonesia's location at the convergence of multiple tectonic plates results in a unique geomorphological feature with abundant hot springs. This study pioneers the metagenomic exploration of Indonesian hot springs, harbouring unique life forms despite high temperatures. The microbial community of hot springs is taxonomically versatile and biotechnologically valuable. 16s rRNA amplicon sequencing of the metagenome is a viable option for the microbiome investigation. This study utilized Oxford Nanopore's long-read 16 S rRNA sequencing for enhanced species identification, improved detection of rare members, and a more detailed community composition profile.<br><br>DATA DESCRIPTION: Water samples were taken from three hot springs of the Bali, Indonesia (i) Angseri, 8.362503&#xa0;S, 115.133452 E; (ii) Banjar, 8.210270&#xa0;S, 114.967063 E; and (iii) Batur, 8.228806&#xa0;S, 115.404829 E. BioLit Genomic DNA Extraction Kit (SRL, Mumbai, India) was used to isolate DNA from water samples. The quantity and quality of the DNA were determined using a NanoDrop&#x2122; spectrophotometer and a Qubit fluorometer (Thermo Fisher Scientific, USA). The library was created using Oxford Nanopore Technology kits, and the sequencing was done using Oxford Nanopore's GridION platform. All sequencing data was obtained in FASTQ files and filtered using NanoFilt software. This dataset is valuable for searching novel bacteria diversity and their existence.},
}
@article {pmid39358771,
year = {2024},
author = {Kawano-Sugaya, T and Arikawa, K and Saeki, T and Endoh, T and Kamata, K and Matsuhashi, A and Hosokawa, M},
title = {A single amplified genome catalog reveals the dynamics of mobilome and resistome in the human microbiome.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {188},
pmid = {39358771},
issn = {2049-2618},
abstract = {BACKGROUND: The increase in metagenome-assembled genomes (MAGs) has advanced our understanding of the functional characterization and taxonomic assignment within the human microbiome. However, MAGs, as population consensus genomes, often aggregate heterogeneity among species and strains, thereby obfuscating the precise relationships between microbial hosts and mobile genetic elements (MGEs). In contrast, single amplified genomes (SAGs) derived via single-cell genome sequencing can capture individual genomic content, including MGEs.<br><br>RESULTS: We introduce the first substantial SAG dataset (bbsag20) from the human oral and gut microbiome, comprising 17,202 SAGs above medium-quality without co-assembly. This collection unveils a diversity of bacterial lineages across 312 oral and 647 gut species, demonstrating different taxonomic compositions from MAGs. Moreover, the SAGs showed cellular-level evidence of the translocation of oral bacteria to the gut. We also identified broad-host-range MGEs harboring antibiotic resistance genes (ARGs), which were not detected in the MAGs.<br><br>CONCLUSIONS: The difference in taxonomic composition between SAGs and MAGs indicates that combining both methods would be effective in expanding the genome catalog. By connecting mobilomes and resistomes in individual samples, SAGs could meticulously chart a dynamic network of ARGs on MGEs, pinpointing potential ARG reservoirs and their spreading patterns in the microbial community. Video Abstract.},
}
@article {pmid39358016,
year = {2024},
author = {Liu, X and Ni, Y and Ye, L and Guo, Z and Tan, L and Li, J and Yang, M and Chen, S and Li, R},
title = {Nanopore strand-specific mismatch enables de novo detection of bacterial DNA modifications.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.279012.124},
pmid = {39358016},
issn = {1549-5469},
abstract = {DNA modifications in bacteria present diverse types and distributions, playing crucial functional roles. Current methods for detecting bacterial DNA modifications via nanopore sequencing typically involve comparing raw current signals to a methylation-free control. In this study, we found that bacterial DNA modification induces errors in nanopore reads. And these errors are found only in one strand but not the other, showing a strand-specific bias. Leveraging this discovery, we developed Hammerhead, a pioneering pipeline designed for de novo methylation discovery that circumvents the necessity of raw signal inference and a methylation-free control. The majority (14 out of 16) of the identified motifs can be validated by raw signal comparison methods or by identifying corresponding methyltransferases in bacteria. Additionally, we included a novel polishing strategy employing duplex reads to correct modification-induced errors in bacterial genome assemblies, achieving a reduction of over 85% in such errors. In summary, Hammerhead enables users to effectively locate bacterial DNA methylation sites from nanopore FASTQ/FASTA reads, thus holds promise as a routine pipeline for a wide range of nanopore sequencing applications, such as genome assembly, metagenomic binning, decontaminating eukaryotic genome assembly, and functional analysis for DNA modifications.},
}
@article {pmid39357373,
year = {2024},
author = {Liu, Y and Zhang, Q and Shi, Y and Hao, Z and Zhan, X},
title = {Anthropogenic activities significantly interfered distribution and co-occurrence patterns of antibiotic resistance genes in a small rural watershed in Southwest China.},
journal = {Ecotoxicology and environmental safety},
volume = {285},
number = {},
pages = {117118},
doi = {10.1016/j.ecoenv.2024.117118},
pmid = {39357373},
issn = {1090-2414},
abstract = {The prevalence and spread of antibiotic resistance genes (ARGs) have been a significant concern for global public health in recent years. Small rural watersheds are the smallest units of factor mobility for agricultural production in China, and their ARG profiles are the best scale of the contamination status, but the mapping and the distribution and diffusion of ARGs in the water and soil of small rural watersheds are inadequate. In this study, based on microbial metagenomics, we invested prevalence maps of 209 ARGs corresponding to typical commonly used antibiotics (including multidrug, aminoglycoside, macrolide-lincosamide-streptogramin B (MLSB), and β-Lactamase) in water and soil in different agricultural types, as well as within water-soil interfaces in small rural watersheds in Southwest China. The results revealed that the most abundant ARGs in water and soil were consistent, but different in subtypes, and anthropogenic activities affect the transport of ARGs between water and soils. Livestock wastewater discharges influenced the diversity and abundance of ARGs in water, while in soil it is planting type and fertilizer management, and thus interfered with the co-occurrence patterns between bacteria and ARGs. Co-occurrence analysis revealed that Proteobacteria, Actinobacteria, and Bacteroidetes were the predominant ARG hosts in water and soil, but soil exhibited a more intricate ARG-bacterial association. Overall, this study provides integrated profiles of ARGs in water and soil influenced by anthropogenic activities at the small watershed scale in a typical rural area and provides a baseline for comparisons of ARGs.},
}
@article {pmid39357281,
year = {2024},
author = {Zhang, J and Gao, T and Chen, G and Liang, Y and Nie, X and Gu, W and Li, L and Tong, H and Huang, W and Lu, T and Bian, Z and Su, L},
title = {Vinegar-processed Schisandra Chinensis enhanced therapeutic effects on colitis-induced depression through tryptophan metabolism.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {135},
number = {},
pages = {156057},
doi = {10.1016/j.phymed.2024.156057},
pmid = {39357281},
issn = {1618-095X},
abstract = {BACKGROUND: Ulcerative colitis (UC) is an inflammatory bowel disease characterized by its incurable nature and undefined etiology, which is often accompanied by a high prevalence of comorbid depression. The gut-brain axis has emerged as a promising treatment target in recent years.<br><br>PURPOSE: This study aimed to investigate how vinegar-processed Schisandra Chinensis (VSC) enhances therapeutic effects on depressive behavior in chronic UC mice.<br><br>METHODS: A chronic UC model was induced in mice using dextran sulfate sodium. The therapeutic effects of both raw and vinegar-processed Schisandra Chinensis on UC and associated depressive symptoms were assessed. Colonic mucosal damage was evaluated using hematoxylin and eosin (H&amp;E) and Alcian blue staining. The integrity of the blood-brain barrier (BBB) and synaptic structures was visualized via transmission electron microscopy (TEM). Enzyme-linked immunosorbent assay (ELISA) was employed to quantify inflammatory cytokine levels in the colon, serum, and brain, while western blotting was performed for protein expression analysis. Additionally, metagenomic analysis was conducted to investigate gut microbiota composition. Nissl staining and immunofluorescence were used to assess hippocampal neuronal damage, and behavioral assessments including the morris water maze, open field test, forced swimming test and tail suspension test, were implemented to evaluate depressive states. Serum metabolites were analyzed using UPLC-MS/MS.<br><br>RESULTS: Both raw and vinegar-processed Schisandra Chinensis significantly upregulated aryl hydrocarbon receptor (AhR), inhibited NF-&#x3ba;B p-p65 activation, and reduced levels of pro-inflammatory cytokine. These treatments also enhanced the expression of tight junction proteins, restored colonic mucosal and BBB integrity, alleviated damage to hippocampal neurons, and improved synaptic structure. Behavioral assessments indicated that VSC was particularly effective in ameliorating depressive-like behaviors in chronic UC mice. In the gut, both treatments reshaped the gut microbial composition, restoring the relative abundance of Duncaniella, Candidatus_Amulumruptor, Alistipes, Parabacteroides, Lachnospiraceae_bacterium, uncultured_Bacteroides_sp., Candidatus_Amulumruptor_caecigallinarius, with VSC showing more pronounced effects. Serum metabolomics revealed an increase in tryptophan levels and a decrease in kynurenine and xanthurenic acid levels with VSC, indicating that tryptophan metabolism shifted from the kynurenine pathway to the 5-HT or indole pathway. However, this phenomenon did not occur with Schisandra Chinensis (SC).<br><br>CONCLUSION: This study demonstrated that the disruption of tryptophan metabolic balance served as a biological mechanism underlying the occurrence of depressive behaviors induced by UC. The application of SC following vinegar processing enhanced its regulatory effects on gut microbiota and tryptophan metabolism. This findings provided a new insight for the clinical management of gut-brain comorbidities.},
}
@article {pmid39357183,
year = {2024},
author = {Thapliyal, P and Sah, V and Rautela, I and Joshi, M and Tyagi, S and Verma, R and Sharma, MD},
title = {Next Generation Sequencing: Latent applications in clinical diagnostics with the advent of bioinformatic frameworks.},
journal = {Pathology, research and practice},
volume = {263},
number = {},
pages = {155606},
doi = {10.1016/j.prp.2024.155606},
pmid = {39357183},
issn = {1618-0631},
abstract = {For the past 3-4 decades, the discovery of Sanger's method of pyrosequencing was the only method unparalleled till 2005 being employed as a method of whole genome sequencing (WGS). Following this, a revolutionary extensive parallel sequencing method, Next Generation Sequencing (NGS), was engineered. NGS supported a substantial number of bases under a high throughput metagenomic interrogation. Bioinformatics contributed notably to this advancement. It provided alignment tools, assembly algorithms, and protocols such as Illumina and hybridization capture which have metamorphosed clinical and translational diagnostics. With the extension in precision medicine and targeted therapy under NGS sectors such as epigenetics, transcriptomics, mutation detection, prognosis, therapeutics, and patient management have been gaining progress. Using NGS in real-time clinical settings has been proven to produce positive outcomes. The most recent instrumental benefaction of NGS has been decoding the SARS-CoV-2 virus epidemiology with the assistance of multiplex PCR. So far, it had been employed to inspect different levels of viral loads from low to mid. This has been executed by amplification and phylogenetic examination of the load to raise a connective link with the evolutionary history leading up to the period of origin. The depletion in the consumed time and extensive genome size under analysis was further coupled by a cutback in the cost of sequencing while executing NGS. With the aid of this review paper, we aspire to manifest how the above-mentioned elements have boosted, tissue, microbial, and molecular data interrogation. Along with this, promoting, and stimulating an extensive evaluation and expansion in the paradigm of morphological and phenotypic study, via bioinformatics can facilitate further advancement in personalized and concise clinical research.},
}
@article {pmid39357157,
year = {2024},
author = {Zhao, Y and Fan, L and Gao, SH and Huang, F and Lei, Z and Wang, W and Gao, R and Dai, Z and Li, Q and Liang, B and Wang, A},
title = {Strain-level multidrug-resistant pathogenic bacteria in urban wastewater treatment plants: Transmission, source tracking and evolution.},
journal = {Water research},
volume = {267},
number = {},
pages = {122538},
doi = {10.1016/j.watres.2024.122538},
pmid = {39357157},
issn = {1879-2448},
abstract = {Wastewater treatment plants (WWTPs) serve as reservoirs for various pathogens and play a pivotal role in safeguarding environmental safety and public health by mitigating pathogen release. Pathogenic bacteria, known for their potential to cause fatal infections, present a significant and emerging threat to global health and remain poorly understood regarding their origins and transmission in the environment. Using metagenomic approaches, we identified a total of 299 pathogens from three full-scale WWTPs. We comprehensively elucidated the occurrence, dissemination, and source tracking of the pathogens across the WWTPs, addressing deficiencies in traditional detection strategies. While indicator pathogens in current wastewater treatment systems such as Escherichia coli are effectively removed, specific drug-resistant pathogens, including Pseudomonas aeruginosa, Pseudomonas putida, and Aeromonas caviae, persist throughout the treatment process, challenging complete eradication efforts. The anoxic section plays a predominant role in controlling abundance but significantly contributes to downstream pathogen diversity. Additionally, evolution throughout the treatment process enhances pathogen diversity, except for upstream transmission, such as A. caviae str. WP8-S18-ESBL-04 and P. aeruginosa PAO1. Our findings highlight the necessity of expanding current biomonitoring indicators for wastewater treatment to optimize treatment strategies and mitigate the potential health risks posed by emerging pathogens. By addressing these research priorities, we can effectively mitigate risks and safeguard environmental safety and public health.},
}
@article {pmid39356745,
year = {2024},
author = {Hartman, SJ and Hibberd, MC and Mostafa, I and Naila, NN and Islam, MM and Zaman, MU and Huq, S and Mahfuz, M and Islam, MT and Mukherji, K and Moghaddam, VA and Chen, RY and Province, MA and Webber, DM and Henrissat, S and Henrissat, B and Terrapon, N and Rodionov, DA and Osterman, AL and Barratt, MJ and Ahmed, T and Gordon, JI},
title = {A microbiome-directed therapeutic food for children recovering from severe acute malnutrition.},
journal = {Science translational medicine},
volume = {16},
number = {767},
pages = {eadn2366},
doi = {10.1126/scitranslmed.adn2366},
pmid = {39356745},
issn = {1946-6242},
mesh = {Humans ; *Severe Acute Malnutrition/diet therapy/therapy ; Infant ; Microbiota ; Male ; Female ; Bangladesh ; Gastrointestinal Microbiome ; },
abstract = {Globally, severe acute malnutrition (SAM), defined as a weight-for-length z-score more than three SDs below a reference mean (WLZ < -3), affects 14 million children under 5 years of age. Complete anthropometric recovery after standard, short-term interventions is rare, with children often left with moderate acute malnutrition (MAM; WLZ -2 to -3). We conducted a randomized controlled trial (RCT) involving 12- to 18-month-old Bangladeshi children from urban and rural sites, who, after initial hospital-based treatment for SAM, received a 3-month intervention with a microbiome-directed complementary food (MDCF-2) or a calorically more dense, standard ready-to-use supplementary food (RUSF). The rate of WLZ improvement was significantly greater in MDCF-2-treated children (P = 8.73 × 10[-3]), similar to our previous RCT of Bangladeshi children with MAM without antecedent SAM (P = 0.032). A correlated meta-analysis of plasma levels of 4520 proteins in both RCTs revealed 215 positively associated with WLZ (largely representing musculoskeletal and central nervous system development) and 44 negatively associated (primarily related to immune activation). Moreover, the positively associated proteins were significantly enriched by MDCF-2 (q = 1.1 × 10[-6]). Characterizing the abundances of 754 bacterial metagenome-assembled genomes in serially collected fecal samples disclosed the effects of acute rehabilitation for SAM on the microbiome and how, during treatment for MAM, specific strains of Prevotella copri function at the intersection between MDCF-2 glycan metabolism and anthropometric recovery. These results provide a rationale for further testing the generalizability of MDCF efficacy and for identifying biomarkers to define treatment responses.},
}
@article {pmid39355420,
year = {2024},
author = {Albin, D and Ramsahoye, M and Kochavi, E and Alistar, M},
title = {PhageScanner: a reconfigurable machine learning framework for bacteriophage genomic and metagenomic feature annotation.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1446097},
pmid = {39355420},
issn = {1664-302X},
abstract = {Bacteriophages are the most prolific organisms on Earth, yet many of their genomes and assemblies from metagenomic sources lack protein sequences with identified functions. While most bacteriophage proteins are structural proteins, categorized as Phage Virion Proteins (PVPs), a considerable number remain unclassified. Complicating matters further, traditional lab-based methods for PVP identification can be tedious. To expedite the process of identifying PVPs, machine-learning models are increasingly being employed. Existing tools have developed models for predicting PVPs from protein sequences as input. However, none of these efforts have built software allowing for both genomic and metagenomic data as input. In addition, there is currently no framework available for easily curating data and creating new types of machine learning models. In response, we introduce PhageScanner, an open-source platform that streamlines data collection for genomic and metagenomic datasets, model training and testing, and includes a prediction pipeline for annotating genomic and metagenomic data. PhageScanner also features a graphical user interface (GUI) for visualizing annotations on genomic and metagenomic data. We further introduce a BLAST-based classifier that outperforms ML-based models and an efficient Long Short-Term Memory (LSTM) classifier. We then showcase the capabilities of PhageScanner by predicting PVPs in six previously uncharacterized bacteriophage genomes. In addition, we create a new model that predicts phage-encoded toxins within bacteriophage genomes, thus displaying the utility of the framework.},
}
@article {pmid39355269,
year = {2024},
author = {Ding, Y and Liu, G and Li, Q and Zou, L and Dai, J and Chongsuvivatwong, V},
title = {Corrigendum: Distribution characteristics of human herpes viruses in the lower respiratory tract and their impact on 30-day mortality in community-acquired pneumonia patients.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1488546},
doi = {10.3389/fcimb.2024.1488546},
pmid = {39355269},
issn = {2235-2988},
abstract = {[This corrects the article DOI: 10.3389/fcimb.2024.1436509.].},
}
@article {pmid39354675,
year = {2024},
author = {Šardzíková, S and Gajewska, M and Gałka, N and Štefánek, M and Baláž, A and Garaiová, M and Holič, R and Świderek, W and Šoltys, K},
title = {Can longer lifespan be associated with gut microbiota involvement in lipid metabolism?.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiae135},
pmid = {39354675},
issn = {1574-6941},
abstract = {Biological aging is linked to altered body composition and reduced neuroactive steroid hormones like dehydroepiandrosterone sulfate (DHEAS), which can stimulate the GABA signaling pathway via gut microbiota. Our study examined the association of gut microbiota with lifespan in mice through comprehensive analysis of its composition and functional involvement in cholesterol sulfate, a precursor of DHEAS, metabolism. We used 16S rRNA and metagenomic sequencing, followed by metabolic pathway prediction and TLC and MALDI-TOF cholesterol sulfate identification. Significant increases in bacteria such as Bacteroides, typical for long-lived and Odoribacter and Colidextribacter, specific for short-lived mice were detected. Furthermore, for males (Rikenella, Alloprevotella) and females (Lactobacillus, Bacteroides), specific bacterial groups emerged as predictors (AUC=1), highlighting sex-specific patterns. Long-lived mice showed a strong correlation of Bacteroides (0.918) with lipid and steroid hormone metabolism, while a negative correlation of GABAergic synapse with body weight (-0.589). We found that several Bacteroides species harboring the sulfotransferase gene and gene cluster for sulfonate donor synthesis are involved in converting cholesterol to cholesterol sulfate, significantly higher in the feces of long-lived individuals. Overall, we suggest that increased involvement of gut bacteria, mainly Bacteroides spp., in cholesterol sulfate synthesis could ameliorate aging through lipid metabolism.},
}
@article {pmid39354646,
year = {2024},
author = {Jochheim, A and Jochheim, FA and Kolodyazhnaya, A and Morice, &#xc9; and Steinegger, M and Söding, J},
title = {Strain-resolved de-novo metagenomic assembly of viral genomes and microbial 16S rRNAs.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {187},
pmid = {39354646},
issn = {2049-2618},
support = {2019R1A6A1A10073437//National Research Foundation of Korea/ ; 031L0185//Bundesministerium f&#xfc;r Bildung und Forschung/ ; 685778/ERC_/European Research Council/International ; },
mesh = {*RNA, Ribosomal, 16S/genetics ; *Genome, Viral/genetics ; *Metagenomics/methods ; *Bacteria/genetics/classification/virology ; Software ; Humans ; Bayes Theorem ; Viruses/genetics/classification ; Metagenome ; },
abstract = {BACKGROUND: Metagenomics is a powerful approach to study environmental and human-associated microbial communities and, in particular, the role of viruses in shaping them. Viral genomes are challenging to assemble from metagenomic samples due to their genomic diversity caused by high mutation rates. In the standard de Bruijn graph assemblers, this genomic diversity leads to complex k-mer assembly graphs with a plethora of loops and bulges that are challenging to resolve into strains or haplotypes because variants more than the k-mer size apart cannot be phased. In contrast, overlap assemblers can phase variants as long as they are covered by a single read.<br><br>RESULTS: Here, we present PenguiN, a software for strain resolved assembly of viral DNA and RNA genomes and bacterial 16S rRNA from shotgun metagenomics. Its exhaustive detection of all read overlaps in linear time combined with a Bayesian model to select strain-resolved extensions allow it to assemble longer viral contigs, less fragmented genomes, and more strains than existing assembly tools, on both real and simulated datasets. We show a 3-40-fold increase in complete viral genomes and a 6-fold increase in bacterial 16S rRNA genes.<br><br>CONCLUSION: PenguiN is the first overlap-based assembler for viral genome and 16S rRNA assembly from large and complex metagenomic datasets, which we hope will facilitate studying the key roles of viruses in microbial communities. Video Abstract.},
}
@article {pmid39354152,
year = {2024},
author = {Freire-Zapata, V and Holland-Moritz, H and Cronin, DR and Aroney, S and Smith, DA and Wilson, RM and Ernakovich, JG and Woodcroft, BJ and Bagby, SC and , and , and Rich, VI and Sullivan, MB and Stegen, JC and Tfaily, MM},
title = {Microbiome-metabolite linkages drive greenhouse gas dynamics over a permafrost thaw gradient.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {39354152},
issn = {2058-5276},
support = {DE-SC0021349//DOE | SC | Biological and Environmental Research (BER)/ ; 2022070//NSF | Directorate for Biological Sciences (BIO)/ ; 2022070//NSF | Directorate for Biological Sciences (BIO)/ ; 2022070//NSF | Directorate for Biological Sciences (BIO)/ ; 2022070//NSF | Directorate for Biological Sciences (BIO)/ ; 2022070//NSF | Directorate for Biological Sciences (BIO)/ ; 2022070//NSF | Directorate for Biological Sciences (BIO)/ ; 2022070//NSF | Directorate for Biological Sciences (BIO)/ ; 2022070//NSF | Directorate for Biological Sciences (BIO)/ ; 2022070//NSF | Directorate for Biological Sciences (BIO)/ ; 2022070//NSF | Directorate for Biological Sciences (BIO)/ ; 2022070//NSF | Directorate for Biological Sciences (BIO)/ ; 2022070//NSF | Directorate for Biological Sciences (BIO)/ ; },
abstract = {Interactions between microbiomes and metabolites play crucial roles in the environment, yet how these interactions drive greenhouse gas emissions during ecosystem changes remains unclear. Here we analysed microbial and metabolite composition across a permafrost thaw gradient in Stordalen Mire, Sweden, using paired genome-resolved metagenomics and high-resolution Fourier transform ion cyclotron resonance mass spectrometry guided by principles from community assembly theory to test whether microorganisms and metabolites show concordant responses to changing drivers. Our analysis revealed divergence between the inferred microbial versus metabolite assembly processes, suggesting distinct responses to the same selective pressures. This contradicts common assumptions in trait-based microbial models and highlights the limitations of measuring microbial community-level data alone. Furthermore, feature-scale analysis revealed connections between microbial taxa, metabolites and observed CO2 and CH4 porewater variations. Our study showcases insights gained by using feature-level data and microorganism-metabolite interactions to better understand metabolic processes that drive greenhouse gas emissions during ecosystem changes.},
}
@article {pmid39354019,
year = {2024},
author = {Oaikhena, AO and Coker, ME and Cyril-Okoh, D and Wicaksono, WA and Olimi, E and Berg, G and Okeke, IN},
title = {The phyllosphere of Nigerian medicinal plants, Euphorbia lateriflora and Ficus thonningii is inhabited by a specific microbiota.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {22806},
pmid = {39354019},
issn = {2045-2322},
mesh = {*Euphorbia ; *Ficus/microbiology ; *Microbiota/genetics ; *Plants, Medicinal/microbiology ; *Bacteria/genetics/classification/isolation &amp; purification ; *RNA, Ribosomal, 16S/genetics ; *Plant Leaves/microbiology ; *Fungi/genetics/classification/isolation &amp; purification ; Nigeria ; Phylogeny ; },
abstract = {The microbiota of medicinal plants is known to be highly specific and can contribute to medicinal activity. However, the majority of plant species have not yet been studied. Here, we investigated the phyllosphere composition of two common Nigerian medicinal plants, Euphorbia lateriflora and Ficus thonningii, by a polyphasic approach combining analyses of metagenomic DNA and isolates. Microbial abundance estimated via qPCR using specific marker gene primers showed that all leaf samples were densely colonized, with up to 10[8] per gram of leaf, with higher bacterial and fungal abundance than Archaea. While no statistically significant differences between both plant species were found for abundance, amplicon sequencing of 16S rRNA and ITS genes revealed distinct microbiota compositions. Only seven of the 27 genera isolated were represented on both plants, e.g. dominant Sphingomonas spp., and numerous members of Xanthomonadaceae and Enterobacteriaceae. The most dominant fungal families on both plants were Cladosporiaceae, Mycosphaerellaceae and Trichosphaeriaceae. In addition, 225 plant-specific isolates were identified, with Pseudomonadota and Enterobacteriaceae being dominant. Interestingly, 29 isolates are likely species previously unknown, and 14 of these belong to Burkholderiales. However, a high proportion, 56% and 40% of the isolates from E. lateriflora and F. thonningii, respectively, were characterized as various Escherichia coli. The growth of most of the bacterial isolates was not influenced by extractable secondary metabolites of plants. Our results suggest that a specific and diverse microbial community inhabits the leaves of both E. lateriflora and F. thonningii, including potentially new species and producers of antimicrobials.},
}
@article {pmid39354003,
year = {2024},
author = {Li, Y and Liu, H and Xiao, Y and Jing, H},
title = {Metagenome sequencing and 982 microbial genomes from Kermadec and Diamantina Trenches sediments.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {1067},
pmid = {39354003},
issn = {2052-4463},
mesh = {*Geologic Sediments/microbiology ; *Metagenome ; *Archaea/genetics ; *Phylogeny ; *Bacteria/genetics/classification ; Genome, Microbial ; Microbiota ; Genome, Archaeal ; },
abstract = {Deep-sea trenches representing an intriguing ecosystem for exploring the survival and evolutionary strategies of microbial communities in the highly specialized deep-sea environments. Here, 29 metagenomes were obtained from sediment samples collected from Kermadec and Diamantina trenches. Notably, those samples covered a varying sampling depths (from 5321 m to 9415 m) and distinct layers within the sediment itself (from 0~40 cm in Kermadec trench and 0~24 cm in Diamantina trench). Through metagenomic binning process, we reconstructed 982 metagenome assembled genomes (MAGs) with completeness >60% and contamination <5%. Within them, completeness of 351 MAGs were >90%, while an additional 331 were >80%. Phylogenomic analysis for the MAGs revealed nearly all of them were distantly related to known cultivated isolates. The abundant bacterial MAGs affiliated to phyla of Proteobacteria, Planctomycetota, Nitrospirota, Acidobacteriota, Actinobacteriota, and Chlorofexota, while the abundant archaeal phyla affiliated with Nanoarchaeota and Thermoproteota. These results provide a dataset available for further interrogation of diversity, distribution and ecological function of deep-sea microbes existed in the trenches.},
}
@article {pmid39352141,
year = {2024},
author = {Coclet, C and Camargo, AP and Roux, S},
title = {MVP: a modular viromics pipeline to identify, filter, cluster, annotate, and bin viruses from metagenomes.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0088824},
doi = {10.1128/msystems.00888-24},
pmid = {39352141},
issn = {2379-5077},
abstract = {While numerous computational frameworks and workflows are available for recovering prokaryote and eukaryote genomes from metagenome data, only a limited number of pipelines are designed specifically for viromics analysis. With many viromics tools developed in the last few years alone, it can be challenging for scientists with limited bioinformatics experience to easily recover, evaluate quality, annotate genes, dereplicate, assign taxonomy, and calculate relative abundance and coverage of viral genomes using state-of-the-art methods and standards. Here, we describe Modular Viromics Pipeline (MVP) v.1.0, a user-friendly pipeline written in Python and providing a simple framework to perform standard viromics analyses. MVP combines multiple tools to enable viral genome identification, characterization of genome quality, filtering, clustering, taxonomic and functional annotation, genome binning, and comprehensive summaries of results that can be used for downstream ecological analyses. Overall, MVP provides a standardized and reproducible pipeline for both extensive and robust characterization of viruses from large-scale sequencing data including metagenomes, metatranscriptomes, viromes, and isolate genomes. As a typical use case, we show how the entire MVP pipeline can be applied to a set of 20 metagenomes from wetland sediments using only 10 modules executed via command lines, leading to the identification of 11,656 viral contigs and 8,145 viral operational taxonomic units (vOTUs) displaying a clear beta-diversity pattern. Further, acting as a dynamic wrapper, MVP is designed to continuously incorporate updates and integrate new tools, ensuring its ongoing relevance in the rapidly evolving field of viromics. MVP is available at https://gitlab.com/ccoclet/mvp and as versioned packages in PyPi and Conda.IMPORTANCEThe significance of our work lies in the development of Modular Viromics Pipeline (MVP), an integrated and user-friendly pipeline tailored exclusively for viromics analyses. MVP stands out due to its modular design, which ensures easy installation, execution, and integration of new tools and databases. By combining state-of-the-art tools such as geNomad and CheckV, MVP provides high-quality viral genome recovery and taxonomy and host assignment, and functional annotation, addressing the limitations of existing pipelines. MVP's ability to handle diverse sample types, including environmental, human microbiome, and plant-associated samples, makes it a versatile tool for the broader microbiome research community. By standardizing the analysis process and providing easily interpretable results, MVP enables researchers to perform comprehensive studies of viral communities, significantly advancing our understanding of viral ecology and its impact on various ecosystems.},
}
@article {pmid39152661,
year = {2024},
author = {Leugger, F and Schmidlin, M and Lüthi, M and Kontarakis, Z and Pellissier, L},
title = {Scanning amplicons with CRISPR-Dx detects endangered amphibians in environmental DNA.},
journal = {Molecular ecology resources},
volume = {24},
number = {8},
pages = {e14009},
doi = {10.1111/1755-0998.14009},
pmid = {39152661},
issn = {1755-0998},
support = {//Swiss Federal Institute for Forest, Snow and Landscape Research/ ; 40B2-0_203550//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; },
mesh = {Animals ; *Amphibians/genetics/classification ; *DNA, Environmental/genetics ; *Endangered Species ; Switzerland ; *Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; DNA Barcoding, Taxonomic/methods ; Ponds ; Biodiversity ; Metagenomics/methods ; },
abstract = {More efficient methods for extensive biodiversity monitoring are required to support rapid measures to address the biodiversity crisis. While environmental DNA (eDNA) metabarcoding and quantitative PCR (qPCR) methods offer advantages over traditional monitoring approaches, their large-scale application is limited by the time and labour required for developing assays and/or for analysis. CRISPR (clustered regularly interspaced short palindromic repeats) diagnostic technologies (Dx) may overcome some of these limitations, but they have been used solely with species-specific primers, restricting their versatility for biodiversity monitoring. Here, we demonstrate the feasibility of designing species-specific CRISPR-Dx assays in silico within a short metabarcoding fragment using a general primer set, a methodology we term 'ampliscanning', for 18 of the 22 amphibian species in Switzerland. We sub-selected nine species, including three classified as regionally endangered, to test the methodology using eDNA sampled from ponds at nine sites. We compared the ampliscanning detections to data from traditional monitoring at these sites. Ampliscanning was successful at detecting target species with different prevalences across the landscape. With only one visit, we detected more species per site than three traditional monitoring visits (visual and acoustic detections by trained experts), in particular more elusive species and previously undocumented but expected populations. Ampliscanning detected 25 species/site combinations compared to 12 with traditional monitoring. Sensitivity analyses showed that larger numbers of field visits and PCR replicates are more important for reliable detection than many technical replicates at the CRISPR-Dx assay level. Given the reduced sampling and analysis effort, our results highlight the benefits of eDNA and CRISPR-Dx combined with universal primers for large-scale monitoring of multiple endangered species across landscapes to inform conservation measures.},
}
@article {pmid39351905,
year = {2024},
author = {Feng, M and Robinson, S and Qi, W and Edwards, A and Stierli, B and van der Heijden, M and Frey, B and Varliero, G},
title = {Microbial genetic potential differs among cryospheric habitats of the Damma glacier.},
journal = {Microbial genomics},
volume = {10},
number = {10},
pages = {},
doi = {10.1099/mgen.0.001301},
pmid = {39351905},
issn = {2057-5858},
mesh = {*Ice Cover/microbiology ; *Ecosystem ; Soil Microbiology ; Nitrogen Fixation/genetics ; Microbiota/genetics ; Metagenomics ; Geologic Sediments/microbiology ; Bacteria/genetics/classification/isolation &amp; purification ; Metagenome ; Nitrogen Cycle/genetics ; },
abstract = {Climate warming has led to glacier retreat worldwide. Studies on the taxonomy and functions of glacier microbiomes help us better predict their response to glacier melting. Here, we used shotgun metagenomic sequencing to study the microbial functional potential in different cryospheric habitats, i.e. surface snow, supraglacial and subglacial sediments, subglacial ice, proglacial stream water and recently deglaciated soils. The functional gene structure varied greatly among habitats, especially for snow, which differed significantly from all other habitats. Differential abundance analysis revealed that genes related to stress responses (e.g. chaperones) were enriched in ice habitat, supporting the fact that glaciers are a harsh environment for microbes. The microbial metabolic capabilities related to carbon and nitrogen cycling vary among cryospheric habitats. Genes related to auxiliary activities were overrepresented in the subglacial sediment, suggesting a higher genetic potential for the degradation of recalcitrant carbon (e.g., lignin). As for nitrogen cycling, genes related to nitrogen fixation were more abundant in barren proglacial soils, possibly due to the presence of Cyanobacteriota in this habitat. Our results deepen our understanding of microbial processes in glacial ecosystems, which are vulnerable to ongoing global warming, and they have implications for downstream ecosystems.},
}
@article {pmid39351368,
year = {2024},
author = {Tolstoganov, I and Chen, Z and Pevzner, P and Korobeynikov, A},
title = {SpLitteR: diploid genome assembly using TELL-Seq linked-reads and assembly graphs.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e18050},
pmid = {39351368},
issn = {2167-8359},
mesh = {*Diploidy ; Animals ; Humans ; Genome, Human/genetics ; Sheep/genetics ; Software ; Sequence Analysis, DNA/methods ; Gastrointestinal Microbiome/genetics ; High-Throughput Nucleotide Sequencing/methods ; Genome/genetics ; },
abstract = {BACKGROUND: Recent advances in long-read sequencing technologies enabled accurate and contiguous de novo assemblies of large genomes and metagenomes. However, even long and accurate high-fidelity (HiFi) reads do not resolve repeats that are longer than the read lengths. This limitation negatively affects the contiguity of diploid genome assemblies since two haplomes share many long identical regions. To generate the telomere-to-telomere assemblies of diploid genomes, biologists now construct their HiFi-based phased assemblies and use additional experimental technologies to transform them into more contiguous diploid assemblies. The barcoded linked-reads, generated using an inexpensive TELL-Seq technology, provide an attractive way to bridge unresolved repeats in phased assemblies of diploid genomes.<br><br>RESULTS: We developed the SpLitteR tool for diploid genome assembly using linked-reads and assembly graphs and benchmarked it against state-of-the-art linked-read scaffolders ARKS and SLR-superscaffolder using human HG002 genome and sheep gut microbiome datasets. The benchmark showed that SpLitteR scaffolding results in 1.5-fold increase in NGA50 compared to the baseline LJA assembly and other scaffolders while introducing no additional misassemblies on the human dataset.<br><br>CONCLUSION: We developed the SpLitteR tool for assembly graph phasing and scaffolding using barcoded linked-reads. We benchmarked SpLitteR on assembly graphs produced by various long-read assemblers and have demonstrated that TELL-Seq reads facilitate phasing and scaffolding in these graphs. This benchmarking demonstrates that SpLitteR improves upon the state-of-the-art linked-read scaffolders in the accuracy and contiguity metrics. SpLitteR is implemented in C++ as a part of the freely available SPAdes package and is available at https://github.com/ablab/spades/releases/tag/splitter-preprint.},
}
@article {pmid39351299,
year = {2024},
author = {Meng, Q and Tang, Z and Yang, F and Shi, J and Liu, T and Cheng, S},
title = {Functional analysis of microorganisms and metabolites in the cecum of different sheep populations and their effects on production traits.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1437250},
pmid = {39351299},
issn = {1664-302X},
abstract = {The purpose of this study was to investigate the effects of intestinal microbiota on the growth and production performance of different groups of sheep, focusing on the role of cecal microbiota in regulating intestinal function, enhancing digestion and absorption, and improving feed utilization. The production performance of MG × STH (Mongolia × Small Tailed Han) F1 hybrids and purebred STH (Small Tailed Han) sheep by measuring various factors, including enzyme activities and VFAs (volatile fatty acids), to analyze changes in cecal fermentation parameters across different sheep groups. Metagenomic and metabolomic sequencing combined with bioinformatics to analyze the cecal contents of the two sheep populations. The study findings indicated that the MG × STH F1 hybrids outperformed the purebred STH in terms of body weight, height, oblique body length, and VFAs (p < 0.05). Additionally, the MG × STH F1 higher levels of protease and cellulase in the cecum compared to the purebred sheep (p < 0.05). Metagenomic analysis identified 4,034 different microorganisms at the species level. Five differential organisms (Akkermansiaceae bacterium, Escherichia coli, unclassified p Firmicutes, Streptococcus equinus, Methanobrevibacter millerae) positively regulated sheep performance. Metabolomics identified 822 differential metabolites indoleacetaldehyde, 2-aminobenzoic acid, phenyl-Alanine, enol-phenylpyruvate and n-acetylserotonin were associated with improved performance of sheep. The combined results from the metagenomic and metabolomic studies suggest a positive correlation between specific microbes and metabolites and the performance of the sheep. In conclusion, the MG × STH F1 hybrids demonstrated superior growth performance compared to the purebred STH sheep. The identified microorganisms and metabolites have promising roles in positively regulating sheep growth and can be considered key targets for enhancing sheep performance.},
}
@article {pmid39351096,
year = {2024},
author = {Yue, Y and Ke, Y and Zheng, J and Wang, Z and Liu, H and Liu, S},
title = {Microbiota-derived tryptophan metabolism and AMPK/mTOR pathway mediate antidepressant-like effect of Shugan Hewei Decoction.},
journal = {Frontiers in pharmacology},
volume = {15},
number = {},
pages = {1466336},
pmid = {39351096},
issn = {1663-9812},
abstract = {INTRODUCTION: Depression is a common psychological disorder, accompanied by a disturbance of the gut microbiota and its metabolites. Recently, microbiota-derived tryptophan metabolism and AMPK/mTOR pathway were found to be strongly linked to the development of depression. Shugan Hewei Decoction (SHD) is a classical anti-depression traditional Chinese medicine formula. Although, we have shown that SHD exerted antidepressant effects via cecal microbiota and cecum NLRP3 inflammasome, the specific mechanism of SHD on metabolism driven by gut microbiota is unknown. In this study, we focus on the tryptophan metabolism and AMPK/mTOR pathway to elucidate the multifaceted mechanisms of SHD.<br><br>METHODS: Male rats were established to the chronic unpredictable stress (CUS)/social isolation for 6&#xa0;weeks, and SHD-L (7.34&#xa0;g/kg/d), SHD-H (14.68&#xa0;g/kg/d), Fructooligosaccharide (FOS) (3.15&#xa0;g/kg/d) were given by intragastric administration once daily during the last 2&#xa0;weeks. Behavioral experiments were carried out to evaluate the model. The colonic content was taken out for shotgun metagenomic sequencing combined with the untargeted metabolomics, the targeted tryptophan metabolomics. ELISA was used to detect the levels of zonula occludens 1 (ZO-1), Occludin in colon, as well as lipopolysaccharide (LPS), diamine oxidase (DAO), D-lactate (DLA) in serum. The expressions of mRNA and proteins of adenosine monophosphate-activated protein kinase (AMPK)/mammalian target of rapamycin (mTOR) pathway of autophagy were examined using RT-qPCR and Western blot in colon.<br><br>RESULTS: SHD modulated gut microbiota function and biological pathways, which were related to tryptophan metabolism. In addition, SHD could regulate microbiota-derived tryptophan production (such as reduction of 3-HK, 3-HAA etc., increment of ILA, IAA etc.), which metabolites belong to kynurenine (KYN) and indole derivatives. Further, SHD reduced intestinal permeability and enhanced the intestinal barrier function. Moreover, SHD could upregulate the levels of AMPK, microtubule associated protein light chain 3 (LC3), autophagy related protein 5 (ATG5) and Beclin1, downregulate the levels of mTOR, p62, promoted autophagy in colon. Spearman's analysis illustrated the close correlation between tryptophan metabolites and intestinal barrier, AMPK/mTOR pathway.<br><br>CONCLUSION: SHD may exert antidepressant-like effects by regulating microbiota-derived tryptophan metabolism, and triggering the AMPK/mTOR pathway of autophagy, enhancing the intestinal barrier function.},
}
@article {pmid39350160,
year = {2024},
author = {Wei, M and Mao, S and Li, S and Gu, K and Gu, D and Bai, S and Lu, X and Li, M},
title = {Comparing the diagnostic value of targeted with metagenomic next-generation sequencing in immunocompromised patients with lower respiratory tract infection.},
journal = {Annals of clinical microbiology and antimicrobials},
volume = {23},
number = {1},
pages = {88},
pmid = {39350160},
issn = {1476-0711},
support = {23YF1431300//Yangfan Project of Science and Technology Commission of Shanghai Municipality/ ; 2022YFC2603800//National Key Research and Development Program/ ; GWVI-11.1-1//3-Year Action Plan for Strengthening Public Health System in Shanghai/ ; },
mesh = {Humans ; *Immunocompromised Host ; *High-Throughput Nucleotide Sequencing/methods ; Male ; Female ; *Metagenomics/methods ; *Respiratory Tract Infections/diagnosis/microbiology ; Middle Aged ; *Bronchoalveolar Lavage Fluid/microbiology ; Aged ; Adult ; Sensitivity and Specificity ; Bacteria/genetics/isolation &amp; purification/classification ; Young Adult ; },
abstract = {BACKGROUND: Accurate identification of the etiology of lower respiratory tract infections (LRTI) is crucial, particularly for immunocompromised patients with more complex etiologies. The advent of next-generation sequencing (NGS) has enhanced the effectiveness of pathogen detection. However, assessments of the clinical diagnostic value of targeted NGS (tNGS) in immunocompromised patients with LRTI are limited.<br><br>METHODS: To evaluate the diagnostic value of tNGS in immunocompromised patients with LRTI, a total of 88 patients, of whom 54 were immunocompromised, were enrolled. These patients underwent tNGS testing of bronchoalveolar lavage fluid (BALF). Results from both metagenomic next-generation sequencing (mNGS) and conventional microbiological tests (CMT) were also available for all participants. The performance of tNGS was assessed by comparing its findings against mNGS, CMT, and the clinical composite diagnosis.<br><br>RESULTS: In the cohort of 88 patients, tNGS showed comparable diagnostic value to mNGS and was significantly superior to CMT. Compared to CMT and composite reference standard, tNGS showed sensitivity of 94.55% and 90.48%, respectively. In immunocompromised patients, despite a more diverse pathogen variety, tNGS maintained similar sensitivity to mNGS and outperformed CMT. tNGS positively influenced etiologic diagnosis and antibiotic decision-making in 72.72% of cases, leading to a change in antibiotic regimen in 17.05% of cases. We also compared the detection of microbial nucleic acids by tNGS with mNGS and found that tNGS could identify 87.99% of the microbial nucleic acids identified by mNGS.<br><br>CONCLUSION: In summary, our study demonstrated that tNGS offers promising clinical diagnostic accuracy in immunocompromised patients, as evidenced by its favorable comparison with CMT, the composite reference standard, and mNGS.},
}
@article {pmid39350124,
year = {2024},
author = {Wang, Y and He, X and Liu, S and Li, X},
title = {Pneumocystis jirovecii and Nocardia pneumonia in a middle-aged male with Nephrotic syndrome: a case report and literature review.},
journal = {BMC infectious diseases},
volume = {24},
number = {1},
pages = {1071},
pmid = {39350124},
issn = {1471-2334},
abstract = {INTRODUCTION: Nephrotic syndrome (NS) is a common chronic kidney disease that is often accompanied by a state of immunodeficiency. Immunosuppression increases the risk of infections, with Pneumocystis jirovecii and Nocardia brasiliensis being two opportunistic pathogens that can cause severe infections in patients with compromised immune function. This study presents a case of a middle-aged male patient with NS concurrently infected with Pneumocystis jirovecii and Nocardia brasiliensis. It aims to synthesize the pertinent diagnostic approaches and treatment experiences. Notably, there have been no reported cases of NS occurring simultaneously with both Pneumocystis jirovecii pneumonia and Nocardia pneumonia.<br><br>CASE PRESENTATION: A 58-year-old male farmer presented to the hospital with a one-week history of persistent fever, cough, and sputum production. His maximum body temperature was recorded at 39&#xa0;&#xb0;C, and he produced yellow viscous sputum. This patient had a one-year history of NS, managed with long-term oral corticosteroid and cyclophosphamide therapy. Admission chest computed tomography displayed interstitial changes in both lungs. After failing to detect any pathogens through routine etiological tests, we successfully identified Nocardia brasiliensis, Pneumocystis jirovecii, and Lodderomyces elongisporus using bronchoscopy-guided sputum samples through metagenomic next-generation sequencing (mNGS) technology. Subsequently, we initiated a combined treatment regimen for the patient using trimethoprim-sulfamethoxazole, meropenem, and moxifloxacin, which yielded remarkable therapeutic outcomes.<br><br>CONCLUSION: The adoption and promotion of mNGS technologies have significantly resolved the difficulty in early pathogen detection, guiding clinicians from empirical to genomic diagnosis, achieving prevention before treatment, and thereby enhancing patient survival rates.},
}
@article {pmid39349736,
year = {2024},
author = {Karačić, S and Suarez, C and Hagelia, P and Persson, F and Modin, O and Martins, PD and Wilén, BM},
title = {Microbial acidification by N, S, Fe and Mn oxidation as a key mechanism for deterioration of subsea tunnel sprayed concrete.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {22742},
pmid = {39349736},
issn = {2045-2322},
mesh = {*Oxidation-Reduction ; *Manganese/metabolism ; *Iron/metabolism ; *Construction Materials/microbiology ; Corrosion ; *Biofilms/growth &amp; development ; Nitrogen/metabolism ; Sulfur/metabolism ; Steel/chemistry ; Bacteria/metabolism/genetics ; Hydrogen-Ion Concentration ; },
abstract = {The deterioration of fibre-reinforced sprayed concrete was studied in the Oslofjord subsea tunnel (Norway). At sites with intrusion of saline groundwater resulting in biofilm growth, the concrete exhibited significant concrete deterioration and steel fibre corrosion. Using amplicon sequencing and shotgun metagenomics, the microbial taxa and surveyed potential microbial mechanisms of concrete degradation at two sites over five years were identified. The concrete beneath the biofilm was investigated with polarised light microscopy, scanning electron microscopy and X-ray diffraction. The oxic environment in the tunnel favoured aerobic oxidation processes in nitrogen, sulfur and metal biogeochemical cycling as evidenced by large abundances of metagenome-assembled genomes (MAGs) with potential for oxidation of nitrogen, sulfur, manganese and iron, observed mild acidification of the concrete, and the presence of manganese- and iron oxides. These results suggest that autotrophic microbial populations involved in the cycling of several elements contributed to the corrosion of steel fibres and acidification causing concrete deterioration.},
}
@article {pmid39349606,
year = {2024},
author = {Guo, X and Lin, S and Zhang, X and Li, M and Wang, Z and Peng, Y and He, X and Liu, J},
title = {Integrated metabolomic and microbiome analysis identifies Cupriavidus metallidurans as a potential therapeutic target for β-thalassemia.},
journal = {Annals of hematology},
volume = {},
number = {},
pages = {},
pmid = {39349606},
issn = {1432-0584},
support = {21B0827//The Hunan Provincial Department of Education/ ; 202201065317//The Hunan Provincial Health Commission/ ; kq2004076//The Changsha Science and Technology Bureau/ ; 81920108004//National Natural Science Foundation of China/ ; },
abstract = {β-thalassemia(β-TH) is an inherited hemoglobin disorder marked by ineffective erythropoiesis, anemia, splenomegaly, and systemic iron overload, predominantly affecting developing countries in tropical and subtropical regions. Despite extensive research on its pathogenesis, the interactions between gut microbiota and metabolites in β-TH remain poorly understood. This study compares fecal metabolomics and metagenomics between wildtype (Wt) and heterozygous Th3/+ mice, a model for non-transfusion-dependent β-thalassemia intermedia. Our results show increased intestinal bilirubin metabolism, with significant elevations in metabolites such as biliverdin, bilirubin, and stercobilin. Metagenomic analysis revealed notable differences in bacterial composition between Th3/+ and Wt mice. Specifically, Cupriavidus metallidurans was identified as a key bacterium that mitigates anemia by reducing liver and spleen iron deposition. This is the first study to ameliorate anemia in mice by altering gut microbiota, presenting new strategies for β-TH management.},
}
@article {pmid39349486,
year = {2024},
author = {Sun, W and Zhang, Y and Guo, R and Sha, S and Chen, C and Ullah, H and Zhang, Y and Ma, J and You, W and Meng, J and Lv, Q and Cheng, L and Fan, S and Li, R and Mu, X and Li, S and Yan, Q},
title = {A population-scale analysis of 36 gut microbiome studies reveals universal species signatures for common diseases.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {96},
pmid = {39349486},
issn = {2055-5008},
support = {5050071720001//Beijing University of Chinese Medicine (BUCM)/ ; 2180072120049//Beijing University of Chinese Medicine (BUCM)/ ; 81503455//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Feces/microbiology ; Case-Control Studies ; *Bacteria/classification/genetics/isolation &amp; purification ; Metagenome ; Metagenomics/methods ; China ; Biodiversity ; },
abstract = {The gut microbiome has been implicated in various human diseases, though findings across studies have shown considerable variability. In this study, we reanalyzed 6314 publicly available fecal metagenomes from 36 case-control studies on different diseases to investigate microbial diversity and disease-shared signatures. Using a unified analysis pipeline, we observed reduced microbial diversity in many diseases, while some exhibited increased diversity. Significant alterations in microbial communities were detected across most diseases. A meta-analysis identified 277 disease-associated gut species, including numerous opportunistic pathogens enriched in patients and a depletion of beneficial microbes. A random forest classifier based on these signatures achieved high accuracy in distinguishing diseased individuals from controls (AUC = 0.776) and high-risk patients from controls (AUC = 0.825), and it also performed well in external cohorts. These results offer insights into the gut microbiome's role in common diseases in the Chinese population and will guide personalized disease management strategies.},
}
@article {pmid39347544,
year = {2024},
author = {Yergaliyev, T and Künzel, S and Hanauska, A and Rees, A and Wild, KJ and Pétursdóttir, &#xc1;H and Gunnlaugsdóttir, H and Reynolds, CK and Humphries, DJ and Rodehutscord, M and Camarinha-Silva, A},
title = {The effect of Asparagopsis taxiformis, Ascophyllum nodosum, and Fucus vesiculosus on ruminal methanogenesis and metagenomic functional profiles in vitro.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0394223},
doi = {10.1128/spectrum.03942-23},
pmid = {39347544},
issn = {2165-0497},
abstract = {UNLABELLED: The ruminant-microorganism symbiosis is unique by providing high-quality food from fibrous materials but also contributes to the production of one of the most potent greenhouse gases-methane. Mitigating methanogenesis in ruminants has been a focus of interest in the past decades. One of the promising strategies to combat methane production is the use of feed supplements, such as seaweeds, that might mitigate methanogenesis via microbiome modulation and direct chemical inhibition. We conducted in vitro investigations of the effect of three seaweeds (Ascophyllum nodosum, Asparagopsis taxiformis, and Fucus vesiculosus) harvested at different locations (Iceland, Scotland, and Portugal) on methane production. We applied metataxonomics (16S rRNA gene amplicons) and metagenomics (shotgun) methods to uncover the interplay between the microbiome's taxonomical and functional states, methanogenesis rates, and seaweed supplementations. Methane concentration was reduced by A. nodosum and F. vesiculosus, both harvested in Scotland and A. taxiformis, with the greatest effect of the latter. A. taxiformis acted through the reduction of archaea-to-bacteria ratios but not eukaryotes-to-bacteria. Moreover, A. taxiformis application was accompanied by shifts in both taxonomic and functional profiles of the microbial communities, decreasing not only archaeal ratios but also abundances of methanogenesis-associated functions. Methanobrevibacter "SGMT" (M. smithii, M. gottschalkii, M. millerae or M. thaueri; high methane yield) to "RO" (M. ruminantium and M. olleyae; low methane yield) clades ratios were also decreased, indicating that A. taxiformis application favored Methanobrevibacter species that produce less methane. Most of the functions directly involved in methanogenesis were less abundant, while the abundances of the small subset of functions that participate in methane assimilation were increased.<br><br>IMPORTANCE: The application of A. taxiformis significantly reduced methane production in vitro. We showed that this reduction was linked to changes in microbial function profiles, the decline in the overall archaeal community counts, and shifts in ratios of Methanobrevibacter "SGMT" and "RO" clades. A. nodosum and F. vesiculosus, obtained from Scotland, also decreased methane concentration in the total gas, while the same seaweed species from Iceland did not.},
}
@article {pmid39347539,
year = {2024},
author = {Yuan, Y and Hu, H and Sun, Z and Wang, W and Wang, Z and Zheng, M and Xing, Y and Zhang, W and Wang, M and Lu, X and Li, Y and Liang, C and Lin, Z and Xie, C and Li, J and Mao, T},
title = {Combining Metagenomics, Network Pharmacology and RNA-Seq Strategies to Reveal the Therapeutic Effects and Mechanisms of Qingchang Wenzhong Decoction on Inflammatory Bowel Disease in Mice.},
journal = {Drug design, development and therapy},
volume = {18},
number = {},
pages = {4273-4289},
pmid = {39347539},
issn = {1177-8881},
mesh = {Animals ; Mice ; *Drugs, Chinese Herbal/pharmacology/chemistry ; *Inflammatory Bowel Diseases/drug therapy ; *Metagenomics ; *Gastrointestinal Microbiome/drug effects ; *Network Pharmacology ; *Dextran Sulfate ; *Mice, Inbred C57BL ; Disease Models, Animal ; Male ; RNA-Seq ; },
abstract = {BACKGROUND: Inflammatory bowel disease (IBD) is a chronic and recurrent inflammatory disease that lacks effective treatments. Qingchang Wenzhong Decoction (QCWZD) is a clinically effective herbal prescription that has been proven to attenuate intestinal inflammation in IBD. However, its molecular mechanism of action has not been clearly elucidated.<br><br>PURPOSE: We aimed to probe the mechanism of QCWZD for the treatment of IBD.<br><br>METHODS: The dextran sulfate sodium (DSS)-induced mouse model of IBD was used to identify the molecular targets involved in the mechanism of action of QCWZD. Metagenomics sequencing was utilized to analyze the differences in gut microbiota and the functional consequences of these changes. Network pharmacology combined with RNA sequencing (RNA-seq) were employed to predict the molecular targets and mechanism of action of QCWZD, and were validated through in vivo experiments.<br><br>RESULTS: Our results demonstrated that QCWZD treatment alleviated intestinal inflammation and accelerated intestinal mucosal healing that involved restoration of microbial homeostasis. This hypothesis was supported by the results of bacterial metagenomics sequencing that showed attenuation of gut dysbiosis by QCWZD treatment, especially the depletion of the pathogenic bacterial genus Bacteroides, while increasing the beneficial microorganism Akkermansia muciniphila that led to altered bacterial gene functions, such as metabolic regulation. Network pharmacology and RNA-seq analyses showed that Th17 cell differentiation plays an important role in QCWZD-based treatment of IBD. This was confirmed by in vivo experiments showing a marked decrease in the percentage of CD3[+]CD4[+]IL-17[+] (Th17) cells. Furthermore, our results also showed that the key factors associated with Th17 cell differentiation (IL-17, NF-&#x3ba;B, TNF-&#x3b1; and IL-6) in the colon were significantly reduced in QCWZD-treated colitis mice.<br><br>CONCLUSION: QCWZD exerted beneficial effects in the treatment of IBD by modulating microbial homeostasis while inhibiting Th17 cell differentiation and its associated pathways, providing a novel and promising therapeutic strategy for the treatment of IBD.},
}
@article {pmid39346682,
year = {2024},
author = {Child, HT and Wierzbicki, L and Joslin, GR and Tennant, RK},
title = {Comparative evaluation of soil DNA extraction kits for long read metagenomic sequencing.},
journal = {Access microbiology},
volume = {6},
number = {9},
pages = {},
pmid = {39346682},
issn = {2516-8290},
abstract = {Metagenomics has been transformative in our understanding of the diversity and function of soil microbial communities. Applying long read sequencing to whole genome shotgun metagenomics has the potential to revolutionise soil microbial ecology through improved taxonomic classification, functional characterisation and metagenome assembly. However, optimisation of robust methods for long read metagenomics of environmental samples remains undeveloped. In this study, Oxford Nanopore sequencing using samples from five commercially available soil DNA extraction kits was compared across four soil types, in order to optimise read length and reproducibility for comparative long read soil metagenomics. Average extracted DNA lengths varied considerably between kits, but longer DNA fragments did not translate consistently into read lengths. Highly variable decreases in the length of resulting reads from some kits were associated with poor classification rate and low reproducibility in microbial communities identified between technical repeats. Replicate samples from other kits showed more consistent conversion of extracted DNA fragment size into read length and resulted in more congruous microbial community representation. Furthermore, extraction kits showed significant differences in the community representation and structure they identified across all soil types. Overall, the QIAGEN DNeasy PowerSoil Pro Kit displayed the best suitability for reproducible long-read WGS metagenomic sequencing, although further optimisation of DNA purification and library preparation may enable translation of higher molecular weight DNA from other kits into longer read lengths. These findings provide a novel insight into the importance of optimising DNA extraction for achieving replicable results from long read metagenomic sequencing of environmental samples.},
}
@article {pmid39346055,
year = {2024},
author = {Knobloch, S and Salimi, F and Buaya, A and Ploch, S and Thines, M},
title = {RAPiD: a rapid and accurate plant pathogen identification pipeline for on-site nanopore sequencing.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e17893},
pmid = {39346055},
issn = {2167-8359},
mesh = {*Nanopore Sequencing/methods ; Metagenomics/methods ; Plant Diseases/microbiology ; Bacteria/genetics/isolation &amp; purification/classification ; Sequence Analysis, DNA/methods ; Fungi/genetics/isolation &amp; purification/classification ; Plants/microbiology ; Computational Biology/methods ; },
abstract = {Nanopore sequencing technology has enabled the rapid, on-site taxonomic identification of samples from anything and anywhere. However, sequencing errors, inadequate databases, as well as the need for bioinformatic expertise and powerful computing resources, have hampered the widespread use of the technology for pathogen identification in the agricultural sector. Here we present RAPiD, a lightweight and accurate real-time taxonomic profiling pipeline. Compared to other metagenomic profilers, RAPiD had a higher classification precision achieved through the use of a curated, non-redundant database of common agricultural pathogens and extensive quality filtering of alignments. On a fungal, bacterial and mixed mock community RAPiD was the only pipeline to detect all members of the communities. We also present a protocol for in-field sample processing enabling pathogen identification from plant sample to sequence within 3 h using low-cost equipment. With sequencing costs continuing to decrease and more high-quality reference genomes becoming available, nanopore sequencing provides a viable method for rapid and accurate pathogen identification in the field. A web implementation of the RAPiD pipeline for real-time analysis is available at https://agrifuture.senckenberg.de.},
}
@article {pmid39346007,
year = {2024},
author = {Eisenhofer, R and Alberdi, A and Woodcroft, BJ},
title = {Quantifying microbial DNA in metagenomes improves microbial trait estimation.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae111},
pmid = {39346007},
issn = {2730-6151},
abstract = {Shotgun metagenomics is a powerful tool for studying the genomic traits of microbial community members, such as genome size, gene content, etc. While such traits can be used to better understand the ecology and evolution of microbial communities, the accuracy of their estimations can be critically influenced by both known and unknown factors. One factor that can bias trait estimations is the proportion of eukaryotic and viral DNA in a metagenome, as some bioinformatic tools assume that all DNA reads in a metagenome are bacterial or archaeal. Here, we add to a recent debate about the influence of eukaryotic DNA in the estimation of average genome size from a global soil sample dataset using a new bioinformatic tool. Contrary to what was assumed, our reanalysis of this dataset revealed that soil samples can contain a substantial proportion of non-microbial DNA, which severely inflated the original estimates of average genome size. Correcting for this bias significantly improves the statistical support for the negative relationship between average bacterial genome size and soil pH. These results highlight that metagenomes can contain large quantities of non-microbial DNA and that new methods that correct for this can improve microbial trait estimation.},
}
@article {pmid39345755,
year = {2024},
author = {Deng, Y and Mao, J and Choi, J and Lê Cao, KA},
title = {StableMate: a statistical method to select stable predictors in omics data.},
journal = {NAR genomics and bioinformatics},
volume = {6},
number = {4},
pages = {lqae130},
pmid = {39345755},
issn = {2631-9268},
abstract = {Identifying statistical associations between biological variables is crucial to understanding molecular mechanisms. Most association studies are based on correlation or linear regression analyses, but the identified associations often lack reproducibility and interpretability due to the complexity and variability of omics datasets, making it difficult to translate associations into meaningful biological hypotheses. We developed StableMate, a regression framework, to address these challenges through a process of variable selection across heterogeneous datasets. Given datasets from different environments, such as experimental batches, StableMate selects environment-agnostic (stable) and environment-specific predictors in predicting the response of interest. Stable predictors represent robust functional dependencies with the response, and can be used to build regression models that make generalizable predictions in unseen environments. We applied StableMate to (i) RNA sequencing data of breast cancer to discover genes that consistently predict estrogen receptor expression across disease status; (ii) metagenomics data to identify microbial signatures that show persistent association with colon cancer across study cohorts; and (iii) single-cell RNA sequencing data of glioblastoma to discern signature genes associated with the development of pro-tumour microglia regardless of cell location. Our case studies demonstrate that StableMate is adaptable to regression and classification analyses and achieves comprehensive characterization of biological systems for different omics data types.},
}
@article {pmid39345370,
year = {2024},
author = {Leon, F and Espinoza-Esparza, JM and Deng, V and Coyle, MC and Espinoza, S and Booth, DS},
title = {Cell differentiation controls iron assimilation in a choanoflagellate.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.05.25.595918},
pmid = {39345370},
issn = {2692-8205},
abstract = {Marine microeukaryotes have evolved diverse cellular features that link their life histories to surrounding environments. How those dynamic life histories intersect with the ecological functions of microeukaryotes remains a frontier to understand their roles in essential biogeochemical cycles [1,2] . Choanoflagellates, phagotrophs that cycle nutrients through filter feeding, provide models to explore this intersection, for many choanoflagellate species transition between life history stages by differentiating into distinct cell types [3-6] . Here we report that cell differentiation in the marine choanoflagellate Salpingoeca rosetta endows one of its cell types with the ability to utilize insoluble ferric colloids for improved growth through the expression of a cytochrome b561 iron reductase (cytb561a). This gene is an ortholog of the mammalian duodenal cytochrome b561 (DCYTB) that reduces ferric cations prior to their uptake in gut epithelia [7] and is part of an iron utilization toolkit that choanoflagellates and their closest living relatives, the animals, inherited from a last common eukaryotic ancestor. In a database of oceanic metagenomes [8,9] , the abundance of cytb561a transcripts from choanoflagellates positively correlates with upwellings, which are a major source of ferric colloids in marine environments [10] . As this predominant form of iron [11,12] is largely inaccessible to cell-walled microbes [13,14] , choanoflagellates and other phagotrophic eukaryotes may serve critical ecological roles by first acquiring ferric colloids through phagocytosis and then cycling this essential nutrient through iron utilization pathways [13-15] . These findings provide insight into the ecological roles choanoflagellates perform and inform reconstructions of early animal evolution where functionally distinct cell types became an integrated whole at the origin of animal multicellularity [16-22] .},
}
@article {pmid39345270,
year = {2023},
author = {Hanssen, F and Gabernet, G and Smith, NH and Mertes, C and Neogi, AG and Brandhoff, L and Ossowski, A and Altmueller, J and Becker, K and Petzold, A and Sturm, M and Stöcker, T and Sivalingam, S and Brand, F and Schmidt, A and Buness, A and Probst, AJ and Motameny, S and Köster, J},
title = {NCBench: providing an open, reproducible, transparent, adaptable, and continuous benchmark approach for DNA-sequencing-based variant calling.},
journal = {F1000Research},
volume = {12},
number = {},
pages = {1125},
pmid = {39345270},
issn = {2046-1402},
mesh = {Humans ; *Benchmarking/methods ; *High-Throughput Nucleotide Sequencing/methods ; *Sequence Analysis, DNA/methods/standards ; Software ; Genome, Human ; Genetic Variation ; Reproducibility of Results ; Genomics/methods ; },
abstract = {We present the results of the human genomic small variant calling benchmarking initiative of the German Research Foundation (DFG) funded Next Generation Sequencing Competence Network (NGS-CN) and the German Human Genome-Phenome Archive (GHGA). In this effort, we developed NCBench, a continuous benchmarking platform for the evaluation of small genomic variant callsets in terms of recall, precision, and false positive/negative error patterns. NCBench is implemented as a continuously re-evaluated open-source repository. We show that it is possible to entirely rely on public free infrastructure (Github, Github Actions, Zenodo) in combination with established open-source tools. NCBench is agnostic of the used dataset and can evaluate an arbitrary number of given callsets, while reporting the results in a visual and interactive way. We used NCBench to evaluate over 40 callsets generated by various variant calling pipelines available in the participating groups that were run on three exome datasets from different enrichment kits and at different coverages. While all pipelines achieve high overall quality, subtle systematic differences between callers and datasets exist and are made apparent by NCBench.These insights are useful to improve existing pipelines and develop new workflows. NCBench is meant to be open for the contribution of any given callset. Most importantly, for authors, it will enable the omission of repeated re-implementation of paper-specific variant calling benchmarks for the publication of new tools or pipelines, while readers will benefit from being able to (continuously) observe the performance of tools and pipelines at the time of reading instead of at the time of writing.},
}
@article {pmid39345197,
year = {2024},
author = {Wei, Y and Zhang, Y and Zhuang, Y and Tang, Y and Nie, H and Haung, Y and Liu, T and Yang, W and Yan, F and Zhu, Y},
title = {Veillonella parvula acts as a pathobiont promoting the biofilm virulence and cariogenicity of Streptococcus mutans in adult severe caries.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0431823},
doi = {10.1128/spectrum.04318-23},
pmid = {39345197},
issn = {2165-0497},
abstract = {Adult severe caries (ASC) brings severe oral dysfunction and treatment difficulties to patients, and yet no clear pathogenic mechanism for it has been found. This study is focused on the composition of dental plaque microbiome profiles in order to identify disease-relevant species and to investigate into their interactions with the S. mutans. Samples of dental plaque were collected for metagenomic analysis. The acidification, aciduricity, oxidative stress tolerance, and gtf (glucosyltransferase) gene expression of S. mutans cocultured with V. parvula which was identified as ASC-related dominant bacterium. The biofilm formation and extracellular exopolysaccharide (EPS) synthesis of dual-strain were analyzed with scanning electron microscopy (SEM), crystal violet (CV) staining, live/dead bacterial staining, and confocal laser scanning microscopy (CLSM). Furthermore, rodent model experiments were performed to validate the in vivo cariogenicity of the dual-species biofilm. The most significantly abundant taxon found associated with ASC was V. parvula. In vitro experiments found that V. parvula can effectively promote S. mutans mature biofilm formation with enhanced acid resistance, hydrogen peroxide detoxicity, and biofilm virulence. Rodent model experiments revealed that V. parvula was incapable of causing disease on its own, but it significantly heightened the biofilm virulence of S. mutans when being co-infected and augmented the progression, quantity, and severity of dental caries. Our findings demonstrated that V. parvula may act as a synergistic pathobiont to modulate the metabolic activity, spatial structure, and pathogenicity of biofilms of S. mutans in the context of ASC.IMPORTANCEAdult severe caries (ASC), as a special type of acute caries, is rarely reported and its worthiness of further study is still in dispute. Yet studies on the etiology of severe caries in adults have not found a clear pathogenic mechanism for it. Knowledge of the oral microbiota is important for the treatment of dental caries. We discovered that the interaction between V. parvula and S. mutans augments the severity of dental caries in vivo, suggesting V. parvula may act as a synergistic pathobiont exacerbating biofilm virulence of S. mutans in ASC. Our findings may improve the understanding of ASC pathogenesis and are likely to provide a basis for planning appropriate therapeutic strategies.},
}
@article {pmid39345178,
year = {2024},
author = {Hernandez-Velazquez, D and Vasquez, MK and Petre, R and Kyndt, JA},
title = {Genome sequences of Mycobacterium sp. Elmwood and accompanying phage, isolated from a public swimming pool in Nebraska.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0089624},
doi = {10.1128/mra.00896-24},
pmid = {39345178},
issn = {2576-098X},
abstract = {Genome sequencing of a non-tuberculosis Mycobacterium species, isolated from a public pool, shows that the genome contains several genes for antibiotic resistance and anti-phage defense, which are absent from other related Mycobacteria. Metagenomic binning also provided the genome of the accompanying phage, which is distinct from other mycobacterial phages.},
}
@article {pmid39344648,
year = {2024},
author = {Taylor, KD and Wood, AC and Rotter, JI and Guo, X and Herrington, DM and Johnson, WC and Post, WS and Tracy, RP and Rich, SS and Malik, S},
title = {Metagenomic Study of the MESA: Detection of Gemella Morbillorum and Association With Coronary Heart Disease.},
journal = {Journal of the American Heart Association},
volume = {},
number = {},
pages = {e035693},
doi = {10.1161/JAHA.124.035693},
pmid = {39344648},
issn = {2047-9980},
abstract = {BACKGROUND: Inflammation is a feature of coronary heart disease (CHD), but the role of proinflammatory microbial infection in CHD remains understudied.<br><br>METHODS AND RESULTS: CHD was defined in the MESA (Multi-Ethnic Study of Atherosclerosis) as myocardial infarction (251 participants), resuscitated arrest (2 participants), and CHD death (80 participants). We analyzed sequencing reads from 4421 MESA participants in the National Heart, Lung, and Blood Institute Trans-Omics for Precision Medicine program using the PathSeq workflow of the Genome Analysis Tool Kit and a 65-gigabase microbial reference. Paired reads aligning to 840 microbes were detected in >1% of participants. The association of the presence of microbe reads with incident CHD (follow-up, ~18&#x2009;years) was examined. First, important variables were ascertained using a single regularized Cox proportional hazard model, examining change of risk as a function of presence of microbe with age, sex, education level, Life's Simple 7, and inflammation. For variables of importance, the hazard ratio (HR) was estimated in separate (unregularized) Cox proportional hazard models including the same covariates (significance threshold Bonferroni corrected P<6&#xd7;10[-5], 0.05/840). Reads from 2 microbes were significantly associated with CHD: Gemella morbillorum (HR, 3.14 [95% CI, 1.92-5.12]; P=4.86&#xd7;10[-6]) and Pseudomonas species NFACC19-2 (HR, 3.22 [95% CI, 2.03-5.41]; P=1.58&#xd7;10[-6]).<br><br>CONCLUSIONS: Metagenomics of whole-genome sequence reads opens a possible frontier for detection of pathogens for chronic diseases. The association of G morbillorum and Pseudomonas species reads with CHD raises the possibilities that microbes may drive atherosclerotic inflammation and that treatments for specific pathogens may provide clinical utility for CHD reduction.},
}
@article {pmid39343535,
year = {2024},
author = {Masuda, N and Kato, S and Ohkuma, M and Endo, K},
title = {Metagenomic Insights into Ecophysiology of Zetaproteobacteria and Gammaproteobacteria in Shallow Zones within Deep-sea Massive Sulfide Deposits.},
journal = {Microbes and environments},
volume = {39},
number = {3},
pages = {},
pmid = {39343535},
issn = {1347-4405},
mesh = {*Sulfides/metabolism ; *Gammaproteobacteria/genetics/classification/isolation &amp; purification ; *Metagenomics ; *Seawater/microbiology ; *Metagenome ; Geologic Sediments/microbiology/chemistry ; Phylogeny ; Ecosystem ; Pacific Ocean ; Oxidation-Reduction ; Microbiota/genetics ; Carbon Cycle ; },
abstract = {Deep-sea massive sulfide deposits serve as energy sources for chemosynthetic ecosystems in dark, cold environments even after hydrothermal activity ceases. However, the vertical distribution of microbial communities within sulfide deposits along their depth from the seafloor as well as their ecological roles remain unclear. We herein conducted a culture-independent metagenomic ana-lysis of a core sample of massive sulfide deposits collected in a hydrothermally inactive field of the Southern Mariana Trough, Western Pacific, by drilling (sample depth: 0.52‍ ‍m below the seafloor). Based on the gene context of the metagenome-assembled genomes (MAGs) obtained, we showed the metabolic potential of as-yet-uncultivated microorganisms, particularly those unique to the shallow zone rich in iron hydroxides. Some members of Gammaproteobacteria have potential for the oxidation of reduced sulfur species (such as sulfide and thiosulfate) to sulfate coupled to nitrate reduction to ammonia and carbon fixation via the Calvin-Benson-Bassham (CBB) cycle, as the primary producers. The Zetaproteobacteria member has potential for iron oxidation coupled with microaerobic respiration. A comparative ana-lysis with previously reported metagenomes from deeper zones (~2‍ ‍m below the seafloor) of massive sulfide deposits revealed a difference in the relative abundance of each putative primary producer between the shallow and deep zones. Our results expand knowledge on the ecological potential of uncultivated microorganisms in deep-sea massive sulfide deposits and provide insights into the vertical distribution patterns of chemosynthetic ecosystems.},
}
@article {pmid39314969,
year = {2024},
author = {Laiho, JE and Oikarinen, S and Morfopoulou, S and Oikarinen, M and Renner, A and Depledge, D and Ross, MC and Gerling, IC and Breuer, J and Petrosino, JF and Plagnol, V and Pugliese, A and Toniolo, A and Lloyd, RE and Hyöty, H and , },
title = {Detection of enterovirus RNA in pancreas and lymphoid tissues of organ donors with type 1 diabetes.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
pmid = {39314969},
support = {R01 AI050237/AI/NIAID NIH HHS/United States ; },
abstract = {AIMS/HYPOTHESIS: The nPOD-Virus group collaboratively applied innovative technologies to detect and sequence viral RNA in pancreas and other tissues from organ donors with type 1 diabetes. These analyses involved the largest number of pancreas samples collected to date.<br><br>METHODS: We analysed pancreas, spleen, pancreatic lymph nodes, and duodenum samples from the following donor groups: a) donors with type 1 diabetes (n=71), with (n=35) or without (n=36) insulin-containing islets, (b) donors with single or double islet autoantibody positivity without diabetes (n=22) and c) autoantibody-negative donors without diabetes (control donors) (n=74). Five research laboratories participated in this collaborative effort using approaches for unbiased discovery of RNA viruses (two RNA-Seq platforms), targeted detection of Enterovirus A-D species using RT-PCR, and tests for virus growth in cell-culture.<br><br>RESULTS: Direct RNA-Seq did not detect virus signal in pancreas samples, whereas RT-PCR detected enterovirus RNA confirmed by sequencing in low amounts in pancreas samples in three of the five donor groups, namely donors with type 1 diabetes with insulin-containing islets, 16% (5/32) donors being positive, donors with single islet autoantibody positivity with 53% (8/15) donors being positive, and non-diabetic donors with 8% (4/49) being enterovirus RNA positive. Detection of enterovirus RNA was significantly more frequent in single islet autoantibody-positive donors compared to donors with type 1 diabetes with insulin-deficient islets (p-value <0.001) and control donors (p-value 0.004). In some donors, pancreatic lymph nodes were also positive. RT-PCR detected enterovirus RNA also in spleen of a small number of donors and virus enrichment in susceptible cell lines before RT-PCR resulted in much higher rate in spleen positivity, particularly in donors with type 1 diabetes. Interestingly, the enterovirus strains detected did not cause a typical lytic infection, possibly reflecting their persistence-prone nature.<br><br>CONCLUSIONS/INTERPRETATION: This was the largest coordinated effort to examine the presence of enterovirus RNA in pancreas of organ donors with type 1 diabetes, using a multitude of assays. These findings are consistent with the notion that both the subjects with type 1 diabetes and those with islet autoantibodies may carry a low-grade enterovirus infection in the pancreas and lymphoid tissues.},
}
@article {pmid39342853,
year = {2024},
author = {Li, Z and He, Y and Zhang, H and Qian, H and Wang, Y},
title = {Biotransformations of arsenic in marine sediments across marginal slope to hadal zone.},
journal = {Journal of hazardous materials},
volume = {480},
number = {},
pages = {135955},
doi = {10.1016/j.jhazmat.2024.135955},
pmid = {39342853},
issn = {1873-3336},
abstract = {Arsenic compounds are accumulating in deep ocean, but their ecological impacts on deep-sea ecosystem remain elusive. We studied 32 sediment cores (101 layers for metagenomes, along with 41 global reference sediment metagenomes) collected from the South China Sea and the Mariana Trench (MT), characterized with high arsenic accumulation in MT. In these metagenomes we revealed a significantly positive correlation between relative abundance of arsenite methyltransferase gene (arsM) and sampling depth, which suggests that arsenic methylation is the most prevalent arsenic biotransformation process in the deep sea. Lower relative abundance of arsenic efflux gene, compared with arsM, indicates that microbes in deep-sea sediments were prone to methylate arsenite and retain it rather than efflux it. Phylogenetic analysis identified seven clades of ArsM proteins, including two new clades derived primarily from deep-sea microorganisms. Five metagenome-assembled genomes containing aioA for arsenite oxidation also harbor carbon fixation genes in the deep-sea sediment layers, suggesting previously unnoticed contribution of arsenite-oxidizing autotrophic bacteria to the carbon cycle. Therefore, deep-sea microorganisms adopt different detoxification and transformation strategies in response to arsenic compounds, which renews our understanding of arsenic in their ecological impacts and potential contribution in deep ocean.},
}
@article {pmid39342753,
year = {2024},
author = {Zou, S and Hu, R and Liang, S and Lu, T and Kang, D and Li, D},
title = {Assessment of health risk of antibiotics resistance genes from human disturbed habitat to wild animals: Metagenomic insights into availability and functional changes of gut microbiome.},
journal = {Ecotoxicology and environmental safety},
volume = {285},
number = {},
pages = {117117},
doi = {10.1016/j.ecoenv.2024.117117},
pmid = {39342753},
issn = {1090-2414},
abstract = {Not all antibiotic resistance genes (ARGs) pose an ecological risk to their host animals. A standard should be developed to study which types of ARGs posed an ecological risk to wild animals under human disturbances (HDs). In this study, the golden snub-nosed monkeys (Rhinopithecus roxellana) were used as sentinel species. According to the animals-associated enrichment, mobility, and pathogenicity, the ARGs in habitat of sentinel species were divided into four levels. If the mobile and pathogenic ARGs that could be collinear with the metagenome-assembled genome (MAGs) in the gut of the sentinel species, the ARGs were defined as Rank I ARGs and they were considered to have ecological risk to sentinel species. Functional genes in the MAGs that collinear with the Rank I ARGs were used to predict the health risks of sentinel species. The ecological risk to sentinel species was present in 0.158 % of the ARGs-contigs in the habitat. Cultivation and villages, but not grazing, agriculture and ecotourism, increased the ecological risk of the ARGs to wild animals, The ability of gut microbiome to acquire mobile and pathogenic ARGs increased, as did the collinear functional genes, and the health risks of the wild animals also enhanced by the disturbances of cultivation and villages. Cultivation and villages increased the nutrient content of the soil, and they had a positive effect on the ecological risk of Rank I ARGs by affecting the mobile genetic elements (MGEs), microbiome and the resistant group in the habitat, which was why the cultivation and villages increased the health risks of wild animals. We proposed that cultivation and living should be controlled, while grazing, agriculture and ecotourism could be developed in nature reserves of wild animals, but the nutrients in the wild animals' habitat should be monitored.},
}
@article {pmid39342656,
year = {2024},
author = {Silva-Solar, S and Viver, T and Wang, Y and Orellana, LH and Knittel, K and Amann, R},
title = {Acidimicrobiia, the actinomycetota of coastal marine sediments: Abundance, taxonomy and genomic potential.},
journal = {Systematic and applied microbiology},
volume = {47},
number = {6},
pages = {126555},
doi = {10.1016/j.syapm.2024.126555},
pmid = {39342656},
issn = {1618-0984},
abstract = {Microbial communities in marine sediments represent some of the densest and most diverse biological communities known, with up to a billion cells and thousands of species per milliliter. Among this taxonomic diversity, the class Acidimicrobiia, within the phylum Actinomycetota, stands out for its consistent presence, yet its limited taxonomic understanding obscures its ecological role. We used metagenome-assembled genomes from a 5-year Arctic fjord sampling campaign and compared them to publicly available Acidimicrobiia genomes using 16S rRNA gene and whole-genome phylogenies, alongside gene prediction and annotation to study their taxonomy and genomic potential. Overall, we provide a taxonomic overview of the class Acidimicrobiia and show its significant prevalence in Isfjorden and Helgoland coastal sediments, representing over 90% of Actinomycetota 16S rRNA gene sequences, and 3-7% of Bacteria. We propose Benthobacter isfjordensis gen. nov., sp. nov., Hadalibacter litoralis gen. nov., sp. nov., and two new species from Ilumatobacter, following SeqCode guidelines. In addition, we report the first in situ quantification of the family Ilumatobacteraceae, revealing its substantial presence (1-6%) in coastal sediments. This work highlights the need of refining the taxonomy of Acidimicrobiia to better understand their ecological contributions.},
}
@article {pmid39342284,
year = {2024},
author = {Seitz, VA and McGivern, BB and Borton, MA and Chaparro, JM and Schipanski, ME and Prenni, JE and Wrighton, KC},
title = {Cover crop root exudates impact soil microbiome functional trajectories in agricultural soils.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {183},
pmid = {39342284},
issn = {2049-2618},
support = {2021-67019-34814//U.S. Department of Agriculture/ ; 2021-67019-34814//U.S. Department of Agriculture/ ; 2021-67019-34814//U.S. Department of Agriculture/ ; 2021-67019-34814//U.S. Department of Agriculture/ ; 2021-67019-34814//U.S. Department of Agriculture/ ; 2021-67019-34814//U.S. Department of Agriculture/ ; 2021-67019-34814//U.S. Department of Agriculture/ ; P30CA046934//Cancer Center Support Grant/ ; P30CA046934//Cancer Center Support Grant/ ; P30CA046934//Cancer Center Support Grant/ ; 507580//Facilities Integrating Collaborations for User Science/ ; 507580//Facilities Integrating Collaborations for User Science/ ; 507580//Facilities Integrating Collaborations for User Science/ ; },
mesh = {*Soil Microbiology ; *Plant Roots/microbiology ; *Crops, Agricultural/microbiology ; *Microbiota ; *Rhizosphere ; *Soil/chemistry ; Bacteria/classification/metabolism/isolation &amp; purification ; Agriculture ; Plant Growth Regulators/metabolism ; Plant Exudates/metabolism ; Sorghum/metabolism/microbiology ; },
abstract = {BACKGROUND: Cover cropping is an agricultural practice that uses secondary crops to support the growth of primary crops through various mechanisms including erosion control, weed suppression, nutrient management, and enhanced biodiversity. Cover crops may elicit some of these ecosystem services through chemical interactions with the soil microbiome via root exudation, or the release of plant metabolites from roots. Phytohormones are one metabolite type exuded by plants that activate the rhizosphere microbiome, yet managing this chemical interaction remains an untapped mechanism for optimizing plant-soil-microbiome interactions. Currently, there is limited understanding on the diversity of cover crop phytohormone root exudation patterns and our aim was to understand how phytochemical signals selectively enrich specific microbial taxa and functionalities in agricultural soils.<br><br>RESULTS: Here, we link variability in cover crop root exudate composition to changes in soil microbiome functionality. Exudate chemical profiles from 4 cover crop species (Sorghum bicolor, Vicia villosa, Brassica napus, and Secale cereal) were used as the chemical inputs to decipher microbial responses. These distinct exudate profiles, along with a no exudate control, were amended to agricultural soil microcosms with microbial responses tracked over time using metabolomes and genome-resolved metatranscriptomes. Our findings illustrated microbial metabolic patterns were unique in response to cover crop exudate inputs over time, particularly by sorghum and cereal rye amended microcosms. In these microcosms, we identify novel microbial members (at the genera and family level) who produced IAA and GA4 over time. Additionally, we identified cover crop exudates exclusively enriched for bacterial nitrite oxidizers, while control microcosms were discriminated for nitrogen transport, mineralization, and assimilation, highlighting distinct changes in microbial nitrogen cycling in response to chemical inputs.<br><br>CONCLUSIONS: We highlight that root exudate amendments alter microbial community function (i.e., N cycling) and microbial phytohormone metabolisms, particularly in response to root exudates isolated from cereal rye and sorghum plants. Additionally, we constructed a soil microbial genomic catalog of microorganisms responding to commonly used cover crops, a public resource for agriculturally relevant microbes. Many of our exudate-stimulated microorganisms are representatives from poorly characterized or novel taxa, revealing the yet to be discovered metabolic reservoir harbored in agricultural soils. Our findings emphasize the tractability of high-resolution multi-omics approaches to investigate processes relevant for agricultural soils, opening the possibility of targeting specific soil biogeochemical outcomes through biological precision agricultural practices that use cover crops and the microbiome as levers for enhanced crop production. Video Abstract.},
}
@article {pmid39342129,
year = {2024},
author = {García-Estrada, DA and Selem-Mojica, N and Martínez-Hernández, A and Lara-Reyna, J and Dávila-Ramos, S and Verdel-Aranda, K},
title = {Diversity of bacterial communities in wetlands of Calakmul Biosphere Reserve: a comparative analysis between conserved and semi-urbanized zones in pre-Mayan Train era.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {376},
pmid = {39342129},
issn = {1471-2180},
support = {No. 320237//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as, M&#xe9;xico/ ; },
abstract = {BACKGROUND: The Calakmul Biosphere Reserve (CBR) is known for its rich animal and plant biodiversity, yet its microbial communities remain largely unknown. The reserve does not possess permanent bodies of water; nevertheless, seasonal depressions associated with fractures create wetlands, known locally as aguadas. Given the recent construction of the Maya train that crosses the CRB, it is essential to assess the biodiversity of its microorganisms and recognize their potential as a valuable source of goods. This evaluation is pivotal in mitigating potential mismanagement of the forest ecosystem. To enhance comprehension of microbial communities, we characterized the microbiota in three different wetlands. Ag-UD1 and Ag-UD2 wetlands are located in a zone without human disturbances, while the third, Ag-SU3, is in a semi-urbanized zone. Sampling was carried out over three years (2017, 2018, and 2019), enabling the monitoring of spatiotemporal variations in bacterial community diversity. The characterization of microbiome composition was conducted using 16S rRNA metabarcoding. Concurrently, the genomic potential of select samples was examined through shotgun metagenomics.<br><br>RESULTS: Statistical analysis of alpha and beta diversity indices showed significant differences among the bacterial communities found in undisturbed sites Ag-UD1 and Ag-UD2 compared to Ag-SU3. However, no significant differences were observed among sites belonging to the undisturbed area. Furthermore, a comparative analysis at the zone level reveals substantial divergence among the communities, indicating that the geographic location of the samples significantly influences these patterns. The bacterial communities in the CBR wetlands predominantly consist of genera from phyla Actinobacteria, Acidobacteria, and Proteobacteria.<br><br>CONCLUSION: This characterization has identified the composition of microbial communities and provided the initial overview of the metabolic capacities of the microbiomes inhabiting the aguadas across diverse conservation zones. The three sites exhibit distinct microbial compositions, suggesting that variables such as chemical composition, natural and anthropogenic disturbances, vegetation, and fauna may play a pivotal role in determining the microbial structure of the aguadas. This study establishes a foundational baseline for evaluating the impact of climatic factors and human interventions on critical environments such as wetlands.},
}
@article {pmid39342083,
year = {2024},
author = {Wang, X and Yao, S and Yang, X and Li, Y and Yu, Z and Huang, J and Wang, J},
title = {Peritoneal dialysis promotes microbial-driven biosynthesis pathways of sesquiterpenes and triterpenes compounds in end-stage renal disease patients.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {377},
pmid = {39342083},
issn = {1471-2180},
support = {32170071//National Natural Science Foundation of China/ ; 32300051//National Natural Science Foundation of China/ ; 2022JJ40663//Natural Science Foundation of Hunan Province/ ; C2023045//Hunan Province Traditional Chinese Medicine Research Program Project/ ; },
abstract = {The concept of the gut-kidney axis is gaining significant attention due to the close relationship between gut microbiota and kidney disease. Peritoneal dialysis is recognized as a crucial renal replacement therapy for end-stage renal disease (ESRD). The alterations in gut microbiota and related mechanisms after receiving this dialysis method are not fully understood. This study conducted shotgun metagenomic sequencing on fecal samples from 11 end-stage renal disease patients who did not receive dialysis (ESRD_N) and 7 patients who received peritoneal dialysis (ESRD_P). After quality control and correlation analysis of the data, our study is aimed at exploring the impact of peritoneal dialysis on the gut microbiota and health of ESRD patients. Our research findings indicate that the complexity and aggregation characteristics of gut microbiota interactions increase in ESRD_P. In addition, the gut microbiota drives the biosynthesis pathways of sesquiterpenes and triterpenes in ESRD_P patients, which may contribute to blood purification and improve circulation. Therefore, our research will lay the foundation for the prevention and treatment of ESRD.},
}
@article {pmid39342060,
year = {2024},
author = {Amin, A and Khan, IU and Amin, M and Fatima, M and Sajjad, W and Shah, TA and Dawoud, TM and Wondmie, GF},
title = {Resurrected microorganisms: a plethora of resting bacteria underway for human interaction.},
journal = {AMB Express},
volume = {14},
number = {1},
pages = {106},
pmid = {39342060},
issn = {2191-0855},
abstract = {Glaciers, which form due to the accumulation of snow, play a crucial role in providing freshwater resources, supporting river systems, and maintaining ecosystem stability. Pakistan is habitat to over 5000 glaciers, primarily located in the Hindukash, Himalaya, and Karakoram mountain ranges. Understanding the microbial communities thriving in these extreme environments becomes of utmost importance. These glaciers offer a unique perspective on extremophile adaptation, as they harbor microorganisms that are capable of surviving and thriving under harsh conditions. Glacial melting poses a significant threat to ancient microbiomes, potentially leading to the resurgence of epidemics and exposure of life to paleomicrobiota. Mostly glacial microbiome is evenly distributed and shows similar diversity. With the threat of resurrection of ages old microbiome and its incorporation into the waters have raised a major concern for revival of epidemics and exposure of life with paleanmicrobiota again. This has led the scientist to deeply observe the bacterial flora embedded in the cryonite holes of glaciers. This study aims to investigate the bacterial diversity within various glaciers of Pakistan using metagenomic techniques. Kamri, Burzil, Siachin, Baltoro, Shigar Basin, Biafo and Panama Glaciers designated from G1 to G7 respectively were chosen from Pakistan. Through rigorous physicochemical analyses, distinct characteristics among glaciers are revealed, including variations in temperature, depth, electrical conductivity, pH levels, and nutrient concentrations. The exploration of alpha diversity, employing metrics such as Chao1, Shannon, Simpson, and Inverse Simpson indices, offers valuable insights into the richness, evenness, and dominance of species within different samples. Beta diversity was calculated by using R software. The vegan package was used for NMSD, cluster and PCoA analysis based on Bray-Curtis distance. PCA analysis was done by using prcomp package from R software. Based on OTU abundance and environmental factor data, DCA analysis was done to determine the linear model from the gradient value (RDA) and the unimodal model (CCA). results were compiled by drawing cluster dendrogram which predicts the patterns of similarity and dissimilarity between different samples. Notably, phyla Proteobacteria emerge as the dominant phylum, accompanied by Actinobacteria, Firmicutes, and Bacteroidetes. The dendrogram shows five clusters, with close similarity between G1 and G4, glacier samples G3 and G8, and G2 and G7. Seasonal variations in glacier physicochemical properties were also observed, with summer samples having shallower depths, lower temperatures, and slightly acidic pH. In contrast, winter samples have higher electrical conductivity and sulfur content. Ultimately, this research provides a foundational framework for comprehending glacier ecosystems, their resident microbial communities, and their broader ecological significance. The study highlights the potential public health risks linked to the release of ancient microorganisms due to climate change, emphasizing the need for comprehensive monitoring and research to mitigate potential public health threats.},
}
@article {pmid39341984,
year = {2024},
author = {Pandolfo, E and Durán-Wendt, D and Martínez-Cuesta, R and Montoya, M and Carrera-Ruiz, L and Vazquez-Arias, D and Blanco-Romero, E and Garrido-Sanz, D and Redondo-Nieto, M and Martin, M and Rivilla, R},
title = {Metagenomic analyses of a consortium for the bioremediation of hydrocarbons polluted soils.},
journal = {AMB Express},
volume = {14},
number = {1},
pages = {105},
pmid = {39341984},
issn = {2191-0855},
support = {TED2021-130996B-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; GREENER Grant agreement 826312//Horizon 2020 Framework Programme/ ; },
abstract = {A bacterial consortium was isolated from a soil in Noblejas (Toledo, Spain) with a long history of mixed hydrocarbons pollution, by enrichment cultivation. Serial cultures of hydrocarbons polluted soil samples were grown in a minimal medium using diesel (1 mL/L) as the sole carbon and energy source. The bacterial composition of the Noblejas Consortium (NC) was determined by sequencing 16S rRNA gene amplicon libraries. The consortium contained around 50 amplicon sequence variants (ASVs) and the major populations belonged to the genera Pseudomonas, Enterobacter, Delftia, Stenotrophomonas, Achromobacter, Acinetobacter, Novosphingobium, Allorhizobium-Neorhizobium-Rhizobium, Ochrobactrum and Luteibacter. All other genera were below 1%. Metagenomic analysis of NC has shown a high abundance of genes encoding enzymes implicated in aliphatic and (poly) aromatic hydrocarbons degradation, and almost all pathways for hydrocarbon degradation are represented. Metagenomic analysis has also allowed the construction of metagenome assembled genomes (MAGs) for the major players of NC. Metatranscriptomic analysis has shown that several of the ASVs are implicated in hydrocarbon degradation, being Pseudomonas, Acinetobacter and Delftia the most active populations.},
}
@article {pmid39341578,
year = {2024},
author = {Gawande, PS and Manigandan, V and Ganesh R, S and Kannan, VR and Ramu, K and Murthy, MVR},
title = {Metagenomic analysis of pathogenic bacteria and virulence factor genes in coastal sediments from highly urbanized cities of India.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {106984},
doi = {10.1016/j.micpath.2024.106984},
pmid = {39341578},
issn = {1096-1208},
abstract = {A metagenomic approach was employed to investigate the diversity and distribution of Virulence Factors Genes (VFGs) and Pathogenic Bacteria (PB) in sediment samples collected from highly urbanized cities along the Indian coastline. Among the study locations, Mumbai, Veraval and Paradeep showed a higher abundance of PB, with Vibrio and Pseudomonas as dominant at the genus level, and Escherichia coli and Pseudomonas aeruginosa at the species level. In total, 295 VFGs were detected across all sediment samples, of which 40 VFGs showed a similarity of ≥ 90% with the Virulence Database (VFDB) and were focused in this study. Among the virulent proteins, twitching motility protein and flagellar P-ring were found to be prevalent and significantly associated with Vibrio spp., and Pseudomonas spp., indicating potential bacterial pathogenicity. This investigation serves as the basis for future studies and provides insights into the comprehensive taxonomic profiles of PB, VFGs and their associated PB in the coastal sediments of India.},
}
@article {pmid39341403,
year = {2024},
author = {Chen, X and Balliew, J and Bauer, CX and Deegan, J and Gitter, A and Hanson, BM and Maresso, AW and Tisza, MJ and Troisi, CL and Rios, J and Mena, KD and Boerwinkle, E and Wu, F},
title = {Revealing patterns of SARS-CoV-2 variant emergence and evolution using RBD amplicon sequencing of wastewater.},
journal = {The Journal of infection},
volume = {},
number = {},
pages = {106284},
doi = {10.1016/j.jinf.2024.106284},
pmid = {39341403},
issn = {1532-2742},
abstract = {OBJECTIVES: Rapid evolution of SARS-CoV-2 has resulted in the emergence of numerous variants, posing significant challenges to public health surveillance. Clinical genome sequencing, while valuable, has limitations in capturing the full epidemiological dynamics of circulating variants in the general population. This study aimed to monitor the SARS-CoV-2 variant community dynamics and evolution using receptor-binding domain (RBD) amplicon sequencing of wastewater samples.<br><br>METHODS: We sequenced wastewater from El Paso, Texas over 17 months, compared the sequencing data with clinical genome data, and performed biodiversity analysis to reveal SARS-CoV-2 variant dynamics and evolution.<br><br>RESULTS: We identified 91 variants and observed waves of dominant variants transitioning from BA.2 to BA.2.12.1, BA.4&amp;5, BQ.1, and XBB.1.5. Comparison with clinical genome sequencing data revealed earlier detection of variants and identification of unreported outbreaks. Our results also showed strong consistency with clinical data for dominant variants at the local, state, and national levels. Alpha diversity analyses revealed significant seasonal variations, with the highest diversity observed in winter. By segmenting the outbreak into lag, growth, stationary, and decline phases, we found higher variant diversity during the lag phase, likely due to lower inter-variant competition preceding outbreak growth.<br><br>CONCLUSIONS: Our findings underscore the importance of low transmission periods in facilitating rapid mutation and variant evolution. Our approach, integrating RBD amplicon sequencing with wastewater surveillance, demonstrates effectiveness in tracking viral evolution and understanding variant emergence, thus enhancing public health preparedness.},
}
@article {pmid39341204,
year = {2024},
author = {Takewaki, D and Kiguchi, Y and Masuoka, H and Manu, MS and Raveney, BJE and Narushima, S and Kurokawa, R and Ogata, Y and Kimura, Y and Sato, N and Ozawa, Y and Yagishita, S and Araki, T and Miyake, S and Sato, W and Suda, W and Yamamura, T},
title = {Tyzzerella nexilis strains enriched in mobile genetic elements are involved in progressive multiple sclerosis.},
journal = {Cell reports},
volume = {},
number = {},
pages = {114785},
doi = {10.1016/j.celrep.2024.114785},
pmid = {39341204},
issn = {2211-1247},
abstract = {Multiple sclerosis (MS) is an autoimmune-demyelinating disease with an inflammatory pathology formed by self-reactive lymphocytes with activated glial cells. Progressive MS, characterized by resistance to medications, significantly differs from the non-progressive form in gut microbiome profiles. After confirming an increased abundance of "Tyzzerella nexilis" in various cohorts of progressive MS, we identified a distinct cluster of T. nexilis strains enriched in progressive MS based on long-read metagenomics. The distinct T. nexilis cluster is characterized by a large number of mobile genetic elements (MGEs) and a lack of defense systems against MGEs. Microbial genes for sulfate reduction and flagella formation with pathogenic implications are specific to this cluster. Moreover, these flagellar genes are encoded on MGEs. Mono-colonization with MGE-enriched T. nexilis made germ-free mice more susceptible to experimental autoimmune encephalomyelitis. These results indicate that the progression of MS may be promoted by MGE-enriched T. nexilis with potentially pathogenic properties.},
}
@article {pmid39341154,
year = {2024},
author = {Gough, EK and Edens, TJ and Carr, L and Robertson, RC and Mutasa, K and Ntozini, R and Chasekwa, B and Geum, HM and Baharmand, I and Gill, SK and Mutasa, B and Mbuya, MNN and Majo, FD and Tavengwa, N and Francis, F and Tome, J and Evans, C and Kosek, M and Prendergast, AJ and Manges, AR and , },
title = {Bifidobacterium longum and microbiome maturation modify a nutrient intervention for stunting in Zimbabwean infants.},
journal = {EBioMedicine},
volume = {108},
number = {},
pages = {105362},
doi = {10.1016/j.ebiom.2024.105362},
pmid = {39341154},
issn = {2352-3964},
abstract = {BACKGROUND: Small-quantity lipid-based nutrient supplements (SQ-LNS), which has been widely tested to reduce child stunting, has largely modest effects to date, but the mechanisms underlying these modest effects are unclear. Child stunting is a longstanding indicator of chronic undernutrition and it remains a prevalent public health problem. The infant gut microbiome may be a key contributor to stunting; and mother and infant fucosyltransferase (FUT) phenotypes are important determinants of infant microbiome composition.<br><br>METHODS: We investigated whether mother-infant FUT status (n&#xa0;=&#xa0;792) and infant gut microbiome composition (n&#xa0;=&#xa0;354 fecal specimens from 172 infants) modified the impact of an infant and young child feeding (IYCF) intervention, that included SQ-LNS, on stunting at age 18 months in secondary analysis of a randomized trial in rural Zimbabwe.<br><br>FINDINGS: We found that the impact of the IYCF intervention on stunting was modified by: (i) mother-infant FUT2+/FUT3- phenotype (difference-in-differences&#xa0;-32.6% [95% CI:&#xa0;-55.3%,&#xa0;-9.9%]); (ii) changes in species composition that reflected microbiome maturation (difference-in-differences&#xa0;-68.1% [95% CI:&#xa0;-99.0%,&#xa0;-28.5%); and (iii) greater relative abundance of B.&#xa0;longum (differences-in-differences 49.1% [95% CI: 26.6%, 73.6%]). The dominant strains of B.&#xa0;longum when the intervention started were most similar to the proficient milk oligosaccharide utilizer subspecies infantis, which decreased with infant age and differed by mother-infant FUT2+/FUT3- phenotypes.<br><br>INTERPRETATION: These findings indicate that a persistently "younger" microbiome at initiation of the intervention reduced its benefits on stunting in areas with a high prevalence of growth restriction.<br><br>FUNDING: Bill and Melinda Gates Foundation, UK DFID/Aid, Wellcome Trust, Swiss Agency for Development and Cooperation, US National Institutes of Health, UNICEF, and Nutricia Research Foundation.},
}
@article {pmid39340864,
year = {2024},
author = {Wang, XW and Tan, X and Dang, CC and Liu, LY and Wang, X and Zhao, ZC and Ren, HY and Liu, BF and Xie, GJ},
title = {Enrichment and characterization of thermophilic anaerobic ammonium oxidizing bacteria from hot spring.},
journal = {Water research},
volume = {267},
number = {},
pages = {122497},
doi = {10.1016/j.watres.2024.122497},
pmid = {39340864},
issn = {1879-2448},
abstract = {Anaerobic ammonium oxidization (Anammox) process plays a crucial role in the global nitrogen cycle and sustainable biological nitrogen removal from wastewater. Although Anammox bacteria have been detected across mesophilic and thermophilic conditions, the direct cultivation of Anammox bacteria from thermal environments has remained elusive. This impedes limiting our understanding of their physiology and ecology in high-temperature habitats. Here, we successfully enriched Anammox bacteria from hot spring sediments at 45 °C, achieving an ammonium oxidation rate of 158.0 mg NH4[+]-N l[-1]d[-1], with the genus 'Candidatus Brocadia' presenting 22.9 % of the total microbial community after about 500 days of operation. Metagenomic analysis recovered two high-quality genomes of novel Anammox bacteria, which we designed as 'Candidatus Brocadia thermophilus' and 'Candidatus Brocadia thermoanammoxidans'. Both of them encoded and actively expressed key metabolic genes involved in Anammox process and several genes associated with thermotolerance, demonstrating their remarkable ability to perform Anammox reaction in thermophilic environments. Notably, phylotypes related to 'Candidatus Brocadia thermoanammoxidans' have frequently been retrieved from geographically distinct natural habitats. These findings expand our understanding of thermophilic Anammox bacteria and underscore their potential in the nitrogen cycle of thermal natural and engineering ecosystems.},
}
@article {pmid39340684,
year = {2024},
author = {Vinothini, K and Nakkeeran, S and Saranya, N and Jothi, P and Richard, JI and Perveen, K and Bukhari, NA and Glick, BR and Sayyed, RZ and Mastinu, A},
title = {Rhizosphere Engineering of Biocontrol Agents Enriches Soil Microbial Diversity and Effectively Controls Root-Knot Nematodes.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {120},
pmid = {39340684},
issn = {1432-184X},
mesh = {Animals ; *Solanum lycopersicum/microbiology/parasitology ; *Soil Microbiology ; *Rhizosphere ; *Bacillus/genetics/physiology ; *Plant Roots/microbiology/parasitology ; *Pest Control, Biological ; Plant Diseases/parasitology/prevention &amp; control/microbiology ; Trichoderma/physiology/genetics ; Tylenchoidea/physiology ; Microbiota ; Antinematodal Agents/pharmacology ; Biological Control Agents/pharmacology ; Bacteria/genetics/classification ; },
abstract = {The root-knot nematode (RKN) causes significant yield loss in tomatoes. Understanding the interaction of biocontrol agents (BCAs)-nematicides-soil microbiomes and RKNs is essential for enhancing the efficacy of biocontrol agents and nematicides to curb RKN damage to crops. The present study aimed to evaluate the in vitro effectiveness of BACa and nematicide against RKN and to apply the amplicon sequencing to assess the interaction of Bacillus velezensis (VB7) and Trichoderma koningiopsis (TK) against RKNs. Metagenomic analysis revealed the relative abundance of three phyla such as Proteobacteria (42.16%), Firmicutes (19.57%), and Actinobacteria (17.69%) in tomato rhizospheres. Those tomato rhizospheres treated with the combined application of B. velezensis VB7 + T. koningiopsis TK and RKN had a greater frequency of diversity and richness than the control. RKN-infested tomato rhizosphere drenched with bacterial and fungal antagonists had the maximum diversity index of bacterial communities. A strong correlation with a maximum number of interconnection edges in the phyla Proteobacteria, Firmicutes, and Actinobacteria was evident in soils treated with both B. velezensis VB7 and T. koningiopsis TK challenged against RKN in infected soil. The present study determined a much greater diversity of bacterial taxa observed in tomato rhizosphere soils treated with B. velezensis VB7 and T. koningiopsis TK than in untreated soil. It is suggested that the increased diversity and abundance of bacterial communities might be responsible for increased nematicidal properties in tomato plants. Hence, the combined applications of B. velezensis VB7 and T. koningiopsis TK can enhance the nematicidal action to curb RKN infecting tomatoes.},
}
@article {pmid39340212,
year = {2024},
author = {Avellaneda-Franco, L and Xie, L and Nakai, M and Barr, JJ and Marques, FZ},
title = {Dietary fiber intake impacts gut bacterial and viral populations in a hypertensive mouse model.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2407047},
doi = {10.1080/19490976.2024.2407047},
pmid = {39340212},
issn = {1949-0984},
mesh = {Animals ; *Gastrointestinal Microbiome ; *Dietary Fiber/administration &amp; dosage ; Mice ; Male ; *Hypertension/virology ; *Mice, Inbred C57BL ; *Bacteria/classification/genetics/isolation &amp; purification ; *Bacteriophages/physiology/genetics ; *Disease Models, Animal ; Angiotensin II/metabolism ; Genome, Viral ; },
abstract = {The gut microbiome is an emerging factor in preventing hypertension, yet the influence of gut bacteriophages, viruses infecting bacteria, on this condition remains unclear. Bacteriophage-bacteria interactions, which impact the gut microbiome, are influenced differentially by temperate and virulent bacteriophages. However, the standard technique for studying viral populations, viral-like particles (VLPs)-metagenomes, often overlook prophages, the intracellular stage of temperate bacteriophages, creating a knowledge gap. To address this, we investigated alterations in extracellular and intracellular bacteriophages, alongside bacterial populations, in the angiotensin II-hypertension model. We sequenced VLPs and bulk DNA from cecal-colonic samples collected from male C57BL/6J mice implanted with minipumps containing saline or angiotensin II. We assembled 106 bacterial and 816 viral genomes and found that gut viral and bacterial populations remained stable between hypertensive and normotensive mice. A higher number of temperate viruses were observed across all treatments. Although temperate viruses outnumbered virulent viruses, sequencing of both VLPs and bulk revealed that virions from virulent viruses were more abundant in the murine gut. We then evaluated the impact of low- and high-fiber intake on gut microbiome composition in the angiotensin II model. Fiber intake significantly influenced the gut microbiome composition and hypertension development. Mice receiving high-fiber had lower blood pressure, a higher bacterial-encoded carbohydrate-associated enzyme, and a higher total relative abundance of temperate viruses than those receiving low-fiber. Our findings suggest that phages are not associated with hypertension development in the angiotensin II model. However, they support a complex diet-bacteria/phage interaction that may be involved in blood pressure regulation.},
}
@article {pmid39339905,
year = {2024},
author = {Chaves, M and Hashish, A and Osemeke, O and Sato, Y and Suarez, DL and El-Gazzar, M},
title = {Evaluation of Commercial RNA Extraction Protocols for Avian Influenza Virus Using Nanopore Metagenomic Sequencing.},
journal = {Viruses},
volume = {16},
number = {9},
pages = {},
doi = {10.3390/v16091429},
pmid = {39339905},
issn = {1999-4915},
support = {AP22VSD&amp;B000C010//United States Department of Agriculture/ ; },
mesh = {Animals ; *Influenza in Birds/virology/diagnosis ; *RNA, Viral/genetics/isolation &amp; purification ; *Nanopore Sequencing/methods ; *Influenza A virus/genetics/isolation &amp; purification/classification ; *Metagenomics/methods ; Birds/virology ; High-Throughput Nucleotide Sequencing/methods ; Poultry/virology ; Chickens/virology ; Nanopores ; },
abstract = {Avian influenza virus (AIV) is a significant threat to the poultry industry, necessitating rapid and accurate diagnosis. The current AIV diagnostic process relies on virus identification via real-time reverse transcription-polymerase chain reaction (rRT-PCR). Subsequently, the virus is further characterized using genome sequencing. This two-step diagnostic process takes days to weeks, but it can be expedited by using novel sequencing technologies. We aim to optimize and validate nucleic acid extraction as the first step to establishing Oxford Nanopore Technologies (ONT) as a rapid diagnostic tool for identifying and characterizing AIV from clinical samples. This study compared four commercially available RNA extraction protocols using AIV-known-positive clinical samples. The extracted RNA was evaluated using total RNA concentration, viral copies as measured by rRT-PCR, and purity as measured by a 260/280 absorbance ratio. After NGS testing, the number of total and influenza-specific reads and quality scores of the generated sequences were assessed. The results showed that no protocol outperformed the others on all parameters measured; however, the magnetic particle-based method was the most consistent regarding CT value, purity, total yield, and AIV reads, and it was less error-prone. This study highlights how different RNA extraction protocols influence ONT sequencing performance.},
}
@article {pmid39339865,
year = {2024},
author = {Chacón, RD and Sánchez-Llatas, CJ and da Costa, AC and Valdeiglesias Ichillumpa, S and Cea-Callejo, P and Marín-Sánchez, O and Astolfi-Ferreira, CS and Santander-Parra, S and Nuñez, LFN and Piantino Ferreira, AJ},
title = {Molecular and Evolutionary Characteristics of Chicken Parvovirus (ChPV) Genomes Detected in Chickens with Runting-Stunting Syndrome.},
journal = {Viruses},
volume = {16},
number = {9},
pages = {},
doi = {10.3390/v16091389},
pmid = {39339865},
issn = {1999-4915},
support = {Article Processing Charge//Universidad de Las Am&#xe9;ricas/ ; 301084/2019-0//Conselho Nacional de Pesquisa e Desenvolvimento Tecnol&#xf3;gico (CNPq)/ ; },
mesh = {Animals ; *Genome, Viral ; *Chickens/virology ; *Phylogeny ; *Poultry Diseases/virology ; *Parvoviridae Infections/veterinary/virology ; *Evolution, Molecular ; Metagenomics ; Parvovirinae/genetics/classification ; Parvovirus/genetics/classification ; },
abstract = {Chicken Parvovirus (ChPV) belongs to the genus Aveparvovirus and is implicated in enteric diseases like runting-stunting syndrome (RSS) in poultry. In RSS, chicken health is affected by diarrhea, depression, and increased mortality, causing significant economic losses in the poultry industry. This study aimed to characterize the ChPV genomes detected in chickens with RSS through a metagenomic approach and compare the molecular and evolutionary characteristics within the Aveparvovirus galliform1 species. The intestinal content of broiler flocks affected with RSS was submitted to viral metagenomics. The assembled prevalent genomes were identified as ChPV after sequence and phylogenetic analysis, which consistently clustered separately from Turkey Parvovirus (TuPV). The strain USP-574-A presented signs of genomic recombination. The selective pressure analysis indicated that most of the coding genes in A. galliform1 are evolving under diversifying (negative) selection. Protein modeling of ChPV and TuPV viral capsids identified high conservancy over the VP2 region. The prediction of epitopes identified several co-localized antigenic peptides from ChPV and TuPV, especially for T-cell epitopes, highlighting the immunological significance of these sites. However, most of these peptides presented host-specific variability, obeying an adaptive scenario. The results of this study show the evolutionary path of ChPV and TuPV, which are influenced by diversifying events such as genomic recombination and selective pressure, as well as by adaptation processes, and their subsequent immunological impact.},
}
@article {pmid39339826,
year = {2024},
author = {Laubscher, F and Kaiser, L and Cordey, S},
title = {SCANellome V2: Update of the Primate Anellovirus Reference Sequences Database.},
journal = {Viruses},
volume = {16},
number = {9},
pages = {},
doi = {10.3390/v16091349},
pmid = {39339826},
issn = {1999-4915},
mesh = {Animals ; *Primates/virology ; *Phylogeny ; *Anelloviridae/genetics/classification ; Humans ; *Genome, Viral ; *Metagenomics/methods ; Databases, Genetic ; Genotype ; Open Reading Frames ; },
abstract = {Anelloviruses are ubiquitous in humans and represent a major component of the human virome. Its best-known representative is Torque teno virus (i.e., the Alphatorquevirus genus), which is considered a potential immunity biomarker. Recent metagenomic investigations revealed not only the extraordinary genomic diversity of anellovirus sequences, but also that co-detection of genera, genotypes, or species seems to be the rule in humans. SCANellome was developed to represent a user-friendly tool to analyze the primate (both human and non-human) anellovirus composition at the genus, species, and genotype level from metagenomics data based on an up-to-date database. This SCANellome update includes >900 additional reference sequences from GenBank. Using a clustering at 90% identity, the FASTA database was updated and generated 134 new representative sequences. Based on ORF1, the analysis of these new sequences indicates the presence of 206 potential new species, including four nonhuman primates, and adds four new non-human primate species which will be the subject of a proposal to the International Committee on Taxonomy of Viruses (ICTV). In addition, SCANellome V2 provides now the user with an interactive up-to-date phylogenetic analysis (of ORF1) to show the distribution among the 12 human and nonhuman primate genera of these new potential species. Finally, the Anelloviridae taxonomy was updated to rename species names in binomial format as required by the ICTV.},
}
@article {pmid39339638,
year = {2024},
author = {Galbács, ZN and Agyemang, ED and Pásztor, G and Takács, AP and Várallyay, &#xc9;},
title = {Viromes of Monocotyledonous Weeds Growing in Crop Fields Reveal Infection by Several Viruses Suggesting Their Virus Reservoir Role.},
journal = {Plants (Basel, Switzerland)},
volume = {13},
number = {18},
pages = {},
doi = {10.3390/plants13182664},
pmid = {39339638},
issn = {2223-7747},
support = {K146087//NKFIH/ ; Flagship Research Group Programme//Hungarian University of Agriculture and Life Sciences/ ; },
abstract = {In 2019, random samples of Panicum miliaceum growing as a weed were surveyed to uncover their virus infections at two locations in Hungary. This pilot study revealed infection with three viruses, two appearing for the first time in the country. As follow-up research, in the summer of 2021, we collected symptomatic leaves of several monocotyledonous plants in the same locations and determined their viromes using small RNA high-throughput sequencing (HTS). As a result, we have identified the presence of wheat streak mosaic virus (WSMV), barley yellow striate mosaic virus (BYSMV), barley virus G (BVG), and two additional viruses, namely Aphis glycines virus 1 (ApGlV1) and Ljubljana dicistrovirus 1 (LDV1), which are described for the first time in Hungary. New hosts of the viruses were identified: Cynodon dactylon is a new host of BYSMV and LDV1, Echinocloa crus-galli is a new host of BVG, ApGlV1 and LDV1, Sorghum halepense is a new host of ApGlV1, and Panicum miliaceum is a new host of LDV1. At the same time, Zea mays is a new host of ApGlV1 and LDV1. Small RNA HTS diagnosed acute infections but failed to detect persistent ones, which could be revealed using RT-PCR. The infection rates at the different locations and plant species were different. The phylogenetic analyses of the sequenced virus variants suggest that the tested monocotyledonous weeds can host different viruses and play a virus reservoir role. Viral spread from the reservoir species relies on the activity of insect vectors, which is why their management requires an active role in plant protection strategies, which need careful planning in the changing environment.},
}
@article {pmid39339601,
year = {2024},
author = {Cheng, X and Li, X and Cai, Z and Wang, Z and Zhou, J},
title = {The Structural and Functional Responses of Rhizosphere Bacteria to Biodegradable Microplastics in the Presence of Biofertilizers.},
journal = {Plants (Basel, Switzerland)},
volume = {13},
number = {18},
pages = {},
doi = {10.3390/plants13182627},
pmid = {39339601},
issn = {2223-7747},
support = {41976126//NSFC/ ; 2023KCXTD052//the Innovation Team Project for Guangdong's Universities/ ; RCJC20200714114433069, KCXFZ20201221173211033, and ZDSYS20230626091459009//the Shenzhen Science and Technology Program/ ; },
abstract = {Biodegradable microplastics (Bio-MPs) are a hot topic in soil research due to their potential to replace conventional microplastics. Biofertilizers are viewed as an alternative to inorganic fertilizers in agriculture due to their potential to enhance crop yields and food safety. The use of both can have direct and indirect effects on rhizosphere microorganisms. However, the influence of the coexistence of "Bio-MPs and biofertilizers" on rhizosphere microbial characteristics remains unclear. We investigated the effects of coexisting biofertilizers and Bio-MPs on the structure, function, and especially the carbon metabolic properties of crop rhizosphere bacteria, using a pot experiment in which polyethylene microplastics (PE-MPs) were used as a reference. The results showed that the existence of both microplastics (MPs) changed the physicochemical properties of the rhizosphere soil. Exposure to MPs also remarkably changed the composition and diversity of rhizosphere bacteria. The network was more complex in the Bio-MPs group. Additionally, metagenomic analyses showed that PE-MPs mainly affected microbial vitamin metabolism. Bio-MPs primarily changed the pathways related to carbon metabolism, such as causing declined carbon fixation/degradation and inhibition of methanogenesis. After partial least squares path model (PLS-PM) analysis, we observed that both materials influenced the rhizosphere environment through the bacterial communities and functions. Despite the degradability of Bio-MPs, our findings confirmed that the coexistence of biofertilizers and Bio-MPs affected the fertility of the rhizosphere. Regardless of the type of plastic, its use in soil requires an objective and scientifically grounded approach.},
}
@article {pmid39338979,
year = {2024},
author = {Opitz-Ríos, C and Burgos-Pacheco, A and Paredes-Cárcamo, F and Campanini-Salinas, J and Medina, DA},
title = {Metagenomics Insight into Veterinary and Zoonotic Pathogens Identified in Urban Wetlands of Los Lagos, Chile.},
journal = {Pathogens (Basel, Switzerland)},
volume = {13},
number = {9},
pages = {},
doi = {10.3390/pathogens13090788},
pmid = {39338979},
issn = {2076-0817},
support = {11230295//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; VRID_FAPPE21-07//Universidad San Sebasti&#xe1;n/ ; VRID_INTER23/02//Universidad San Sebasti&#xe1;n/ ; VRID_DocI22/06//Universidad San Sebasti&#xe1;n/ ; },
abstract = {Wetlands are ecosystems that are essential to ecological balance and biodiversity; nevertheless, human activity is a constant threat to them. Excess nutrients are caused by intensive livestock and agricultural operations, pollution, and population growth, which in turn leads to uncontrolled microbiological development. This impairment in water quality can constitute a risk to animal, human, and environmental health. To thoroughly characterize the microbial communities, shotgun metagenomics was used to characterize the taxonomic and functional pattern of microorganisms that inhabit urban wetlands in the Los Lagos Region of Chile. The main objective was to identify microorganisms of veterinary relevance, assess their potential antibiotic resistance, and characterize the main virulence mechanism. As expected, a high diversity of microorganisms was identified, including bacteria described as animal or human pathogens, such as Pasteurella multocida, Pseudomonas aeruginosa, Staphylococcus aureus, and Escherichia coli. Also, a diverse repertory of antimicrobial-resistant genes (ARGs) was detected in metagenomic assembled sequences and inside the sequence of mobile genetic elements, genes that confer mainly resistance to beta-lactams, consistent with the families of antibiotics most used in Chile. In addition, a diverse collection of virulence mechanisms was also identified. Given the significance of the relationship between environmental, animal, and human health-a concept known as One Health-there is a need to establish molecular surveillance programs that monitor the environmental biohazard elements using molecular tools. This work is the first report of the presence of these harmful biological elements in urban wetlands subjected to anthropogenic pressure, located in the south of Chile.},
}
@article {pmid39338934,
year = {2024},
author = {Rimoldi, SG and Tamoni, A and Rizzo, A and Longobardi, C and Pagani, C and Salari, F and Matinato, C and Vismara, C and Gagliardi, G and Cutrera, M and Gismondo, MR},
title = {Evaluation of 16S-Based Metagenomic NGS as Diagnostic Tool in Different Types of Culture-Negative Infections.},
journal = {Pathogens (Basel, Switzerland)},
volume = {13},
number = {9},
pages = {},
doi = {10.3390/pathogens13090743},
pmid = {39338934},
issn = {2076-0817},
abstract = {Bacterial infections pose significant global health challenges, often underestimated due to difficulties in accurate diagnosis, especially when culture-based diagnostics fail. This study assesses the effectiveness of 16S-based metagenomic next generation sequencing (NGS) for identifying pathogens in culture-negative clinical samples across various medical settings. Overall, 48% of samples were collected from orthopedics, 15% from neurosurgery, and 12% in cardiac surgery, among others. The detection rate of monomicrobial infections was 68.6%, and 5.7% for polymicrobial infections. In addition, NGS detected bacteria in all samples from the lungs, head and neck, and eye specimens. Cutibacterium acnes (11%, 12/105) was the most frequent microorganism, followed by Staphylococcus epidermidis (10.4%, 11/105), and Staphylococcus aureus (9.5%, 10/105). In conclusion, 16S-targeted metagenomic sequencing enhances pathogen detection capabilities, particularly in instances where traditional cultures fail. By the combination of NGS and bacterial cultures, microbiologists might provide a more accurate diagnosis, guiding more effective treatments and potentially reducing healthcare costs associated with empirical treatments.},
}
@article {pmid39338575,
year = {2024},
author = {Yin, X and Chen, H and Jiang, K and Zhang, B and Li, R and Zhu, X and Sun, L and Ng, ZL and Su, M},
title = {Distribution Characteristics of Nitrogen-Cycling Microorganisms in Deep-Sea Surface Sediments of Western South China Sea.},
journal = {Microorganisms},
volume = {12},
number = {9},
pages = {},
doi = {10.3390/microorganisms12091901},
pmid = {39338575},
issn = {2076-2607},
support = {2023B1111050014//Guangdong Key Areas R &amp; D Project/ ; SML2021SP307//Project supported by Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; 23qnpy96//Fundamental Research Funds for the Central Universities, Sun Yat-sen University/ ; 24xkjc010//Fundamental Research Funds for the Central Universities, Sun Yat-sen University/ ; },
abstract = {Nitrogen-cycling processes in the deep sea remain understudied. This study investigates the distribution of nitrogen-cycling microbial communities in the deep-sea surface sediments of the western South China Sea, using metagenomic sequencing and real-time fluorescent quantitative PCR techniques to analyze their composition and abundance, and the effects of 11 environmental parameters, including NH4[+]-N, NO3[-]-N, NO2[-]-N, PO4[3-]-P, total nitrogen (TN), total organic carbon (TOC), C/N ratio, pH, electrical conductivity (EC), SO4[2-], and Cl[-]. The phylum- and species-level microbial community compositions show that five sites can be grouped as a major cluster, with sites S1 and S9 forming a sub-cluster, and sites S13, S19, and S26 forming the other; whereas sites S3 and S5 constitute a separate cluster. This is also evident for nitrogen-cycling functional genes, where their abundance is influenced by distinct environmental conditions, including water depths (shallower at sites S1 and S9 against deeper at sites S13, S19, and S26) and unique geological features (sites S3 and S5), whereas the vertical distribution of nitrogen-cycling gene abundance generally shows a decreasing trend against sediment depth. Redundancy analysis (RDA) exploring the correlation between the 11 environmental parameters and microbial communities revealed that the NO2[-]-N, C/N ratio, and TN significantly affect microbial community composition (p < 0.05). This study assesses the survival strategies of microorganisms within deep-sea surface sediments and their role in the marine nitrogen cycle.},
}
@article {pmid39338573,
year = {2024},
author = {Chen, S and Fang, Y and Fujita, R and Khater, EIM and Li, Y and Wang, W and Qian, P and Huang, L and Guo, Z and Zhang, Y and Li, S},
title = {An Exploration of the Viral Coverage of Mosquito Viromes Using Meta-Viromic Sequencing: A Systematic Review and Meta-Analysis.},
journal = {Microorganisms},
volume = {12},
number = {9},
pages = {},
doi = {10.3390/microorganisms12091899},
pmid = {39338573},
issn = {2076-2607},
support = {No.32161143036, No.32311540013//National Natural Science Foundation of China/ ; No. 2022FY100900, 2022FY100904//the Science &amp; Technology Fundamental Resources Investigation Program/ ; No. GWVI-11.1-12//Three-Year Initiative Plan for Strengthening Public Health System Construction in Shanghai (2023-2025) Key Discipline Project/ ; },
abstract = {The aim of this review was to delve into the extent of mosquito virome coverage (proportion of viral reads) via meta-viromic sequencing and uncover potential factors of heterogeneity that could impact this coverage. Data sources were PubMed, Web of Science, Embase, Scopus, Science-Direct, Google Scholar, and the China National Knowledge Infrastructure. Pooled coverage was estimated using random-effects modeling, and subgroup analyses further reveal potential heterogeneous factors. Within the three mosquito genera studied, Culex exhibited the highest pooled viral coverage of mosquito viromes at 7.09% (95% CI: 3.44-11.91%), followed by Anopheles at 5.28% (95% CI: 0.45-14.93%), and Aedes at 2.11% (95% CI: 0.58-7.66%). Subgroup analyses showed that multiple processing methods significantly affected the viral coverage of mosquito viromes, especially pre-treatment of mosquito samples with saline buffer/medium and antibiotics prior to DNase/RNase treatment and removal of the host genome prior to RNA library construction. In conclusion, the results of this study demonstrate that the viral coverage of mosquito viromes varies between mosquito genera and that pre-treatment of mosquito samples with saline buffer/medium and antibiotics before DNase/RNase treatment and removing host genomes prior to RNA library construction are critical for the detection of RNA viruses in mosquito vectors using meta-viromic sequencing.},
}
@article {pmid39338498,
year = {2024},
author = {Liborio, MP and Harris, PNA and Ravi, C and Irwin, AD},
title = {Getting Up to Speed: Rapid Pathogen and Antimicrobial Resistance Diagnostics in Sepsis.},
journal = {Microorganisms},
volume = {12},
number = {9},
pages = {},
doi = {10.3390/microorganisms12091824},
pmid = {39338498},
issn = {2076-2607},
abstract = {Sepsis is a life-threatening organ dysfunction caused by a dysregulated host response to infection. Time to receive effective therapy is a primary determinant of mortality in patients with sepsis. Blood culture is the reference standard for the microbiological diagnosis of bloodstream infections, despite its low sensitivity and prolonged time to receive a pathogen detection. In recent years, rapid tests for pathogen identification, antimicrobial susceptibility, and sepsis identification have emerged, both culture-based and culture-independent methods. This rapid narrative review presents currently commercially available approved diagnostic molecular technologies in bloodstream infections, including their clinical performance and impact on patient outcome, when available. Peer-reviewed publications relevant to the topic were searched through PubMed, and manufacturer websites of commercially available assays identified were also consulted as further sources of information. We have reviewed data about the following technologies for pathogen identification: fluorescence in situ hybridization with peptide nucleic acid probes (Accelerate Pheno[TM]), microarray-based assay (Verigene[®]), multiplex polymerase chain reaction (cobas[®] eplex, BioFire[®] FilmArray[®], Molecular Mouse, Unyvero BCU System[TM]), matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (Rapid MBT Sepsityper[®]), T2 magnetic resonance (T2Bacteria Panel), and metagenomics-based assays (Karius[©], DISQVER[®], Day Zero Diagnostics). Technologies for antimicrobial susceptibility testing included the following: Alfed 60 AST[TM], VITEK[®] REVEAL[TM], dRAST[TM], ASTar[®], Fastinov[®], QuickMIC[®], Resistell[TM], and LifeScale. Characteristics, microbiological performance, and issues of each method are described, as well as their clinical performance, when available.},
}
@article {pmid39338467,
year = {2024},
author = {Wang, Z and Sun, J and Yang, P and Zhang, W and Jiang, Y and Liu, Q and Yang, Y and Hao, R and Guo, G and Huo, W and Zhang, Q and Li, Q},
title = {Molecular Analysis of Indole and Skatole Decomposition Metabolism in Acinetobacter piscicola p38 Utilizing Biochemical and Omics Approaches.},
journal = {Microorganisms},
volume = {12},
number = {9},
pages = {},
doi = {10.3390/microorganisms12091792},
pmid = {39338467},
issn = {2076-2607},
support = {20211331-15//the Shanxi Province "1331 Project" funded project (20211331-15)/ ; },
abstract = {Indole and skatole (3-methylindole, C9H9N) are common nitrogen-containing heterocyclic pollutants found in waste, wastewater treatment plants, and public restrooms and are the most notorious compounds in animal feces. Biodegradation was considered a feasible method for the removal of indole and skatole, but a comprehensive understanding of the metabolic pathways under both aerobic and anaerobic conditions was lacking, and the functional genes responsible for skatole biodegradation remained a mystery. Through metagenomic and gene cluster functional analysis, Acinetobacter piscicola p38 (NCBI: CP167896), genes 1650 (styrene monooxygenase: ACDW34_08180), and 1687 (styrene monooxygenase: ACDW34_08350) were identified as having the potential to degrade indole and skatole. The heterologous expression results demonstrate that the genes 1650 and 1651 (flavin reductase: ACDW34_08185), when combined, are capable of degrading indole, while the genes 1687 and 1688 (flavin reductase: ACDW34_08355), in combination, can degrade indole as well as skatole. These reactions necessitate the involvement of flavin reductase and NAD(P)H to catalyze the oxygenation process. This work aimed to provide new experimental evidence for the biodegradation of indole and skatole. This study offered new insights into our understanding of skatole degradation. The Acinetobacter_piscicola p38 strain provided an effective bacterial resource for the bioremediation of fecal indole and skatole.},
}
@article {pmid39338426,
year = {2024},
author = {Guimarães, LO and Bahia, SL and Ribeiro, GO and Ramos, EDSF and Villanova, F and Dos Santos Morais, V and Telles-de-Deus, J and Helfstein, VC and Santos, JMD and Pandey, RP and Deng, X and Delwart, E and Camargo-Neves, VLF and da Costa, AC and Kirchgatter, K and Leal, &#xc9;},
title = {New Iflavirus Species Characterized from Mosquitoes Captured in the Sao Paulo Zoological Facilities.},
journal = {Microorganisms},
volume = {12},
number = {9},
pages = {},
doi = {10.3390/microorganisms12091749},
pmid = {39338426},
issn = {2076-2607},
support = {2017/50345-5//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2018/16232-1//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 309396/2021-2//National Council for Scientific and Technological Development/ ; },
abstract = {Metagenomic studies of mosquito viromes demonstrated a more diverse composition than just an exclusive composition of pathogenic arboviruses transmitted to humans. In our study, the virome of 866 female mosquitoes collected throughout 2020 at the São Paulo Zoo, located in the city of São Paulo/SP-Brazil, was obtained. Specifically, in this paper, we describe a new virus found by viral RNA extraction and next-generation MiSeq sequencing of a group of 23 specimens of Anopheles (Nys.) strodei. The complete genome with a length of 9709 nucleotides was characterized by a positive orientation and a single strand, with a single large ORF, which encodes a polyprotein of 2987 amino acids. The phylogenetic analysis showed an association with the viral family Iflaviridae and the Riboviria realm. We carried out comparisons with translated sequences of the capsid regions of other iflavirus, and the identities in relation to our sequence were below the minimum limit of 90%, indicating that possibly it is a new species of iflavirus. Our findings contribute to expanding knowledge of virome composition among mosquito species in Brazil and globally. Moreover, we provide a viral genome reference specific to this geographic region and Culicidae family of mosquitoes. This resource facilitates future in silico recognition and assembly of viral genomes within metagenomic datasets.},
}
@article {pmid39338129,
year = {2024},
author = {Mayer, MH and Woldemariam, S and Gisinger, C and Dorner, TE},
title = {Association of Gut Microbiome with Muscle Mass, Muscle Strength, and Muscle Performance in Older Adults: A Systematic Review.},
journal = {International journal of environmental research and public health},
volume = {21},
number = {9},
pages = {},
doi = {10.3390/ijerph21091246},
pmid = {39338129},
issn = {1660-4601},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Sarcopenia/microbiology/physiopathology ; *Muscle Strength ; Aged ; *Muscle, Skeletal/microbiology/physiology ; Middle Aged ; Aged, 80 and over ; },
abstract = {Sarcopenia, characterized by reduced muscle mass, strength, or performance, is a common condition in older adults. The association between the gut microbiome and sarcopenia remains poorly understood. This systematic review aims to evaluate the relationship between muscle parameters and the intestinal microbiome. A systematic search was conducted in PubMed, EMBASE, Cochrane Library, and Google Scholar for studies published between 2002 and 2022 involving participants aged 50+. Studies were included if they assessed sarcopenia using at least one measure of muscle mass (skeletal muscle mass, bioelectrical impedance analysis, MRI), muscle strength, or muscle performance (SARC-F questionnaire, Timed-Up-and-Go Test, Chair Stand Test, grip strength, gait speed, Short Physical Performance Battery, 400 m Walk Test). The microbiome was measured using at least RNA/DNA sequencing or shotgun metagenomic sequencing. Twelve studies were analyzed. Findings revealed that a higher abundance of bacterial species such as Desulfovibrio piger, and Clostridium symbiosum and reduced diversity of butyrate-producing bacteria was associated with sarcopenia severity, as indicated by decreased grip strength, muscle mass, or physical performance. The gut microbiome plays a significant role in age-related muscle loss. Probiotics, prebiotics, and bacterial products could be potential interventions to improve muscle health in older adults.},
}
@article {pmid39336713,
year = {2024},
author = {Dyall-Smith, M and Pfeiffer, F},
title = {Global Distribution and Diversity of Haloarchaeal pL6-Family Plasmids.},
journal = {Genes},
volume = {15},
number = {9},
pages = {},
doi = {10.3390/genes15091123},
pmid = {39336713},
issn = {2073-4425},
mesh = {*Plasmids/genetics ; Phylogeny ; Halobacteriaceae/genetics ; Australia ; Metagenome ; Argentina ; Spain ; Base Composition/genetics ; Puerto Rico ; Genetic Variation ; },
abstract = {Australian isolates of Haloquadratum walsbyi, a square-shaped haloarchaeon, often harbor small cryptic plasmids of the pL6-family, approximately 6 kb in size, and five examples have been previously described. These plasmids exhibit a highly conserved gene arrangement and encode replicases similar to those of betapleolipoviruses. To assess their global distribution and recover more examples for analysis, fifteen additional plasmids were reconstructed from the metagenomes of seven hypersaline sites across four countries: Argentina, Australia, Puerto Rico, and Spain. Including the five previously described plasmids, the average plasmid size is 6002 bp, with an average G+C content of 52.5%. The tetramers GGCC and CTAG are either absent or significantly under-represented, except in the two plasmids with the highest %G+C. All plasmids share a similar arrangement of genes organized as outwardly facing replication and ATPase modules, but variations were observed in some core genes, such as F2, and some plasmids had acquired accessory genes. Two plasmids, pCOLO-c1 and pISLA-c6, shared 92.7% nt identity despite originating from Argentina and Spain, respectively. Numerous metagenomic CRISPR spacers matched sequences in the fifteen reconstructed plasmids, indicating frequent invasion of haloarchaea. Spacers could be assigned to haloarchaeal genera by mapping their associated direct repeats (DR), with half of these matching Haloquadratum. Finally, strand-specific metatranscriptome (RNA-seq) data could be used to demonstrate the active transcription of two pL6-family plasmids, including antisense transcripts.},
}
@article {pmid39335716,
year = {2024},
author = {Thomas-White, K and Hilt, EE and Olmschenk, G and Gong, M and Phillips, CD and Jarvis, C and Sanford, N and White, J and Navarro, P},
title = {A Metagenomics Pipeline to Characterize Self-Collected Vaginal Microbiome Samples.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {14},
number = {18},
pages = {},
doi = {10.3390/diagnostics14182039},
pmid = {39335716},
issn = {2075-4418},
abstract = {Vaginitis is a widespread issue for women worldwide, yet current diagnostic tools are lacking. Bacterial vaginosis (BV) is the most prevalent type of vaginitis, found in 10-50% of reproductive-aged women. Current diagnostic methods for BV rely on clinical criteria, microscopy, or the detection of a few microbes by qPCR. However, many vaginal infections lack a single etiological agent and are characterized by changes in the vaginal microbiome community structure (e.g., BV is defined as a loss of protective lactobacilli resulting in an overgrowth of anaerobic bacteria). Shotgun metagenomic sequencing provides a comprehensive view of all the organisms present in the vaginal microbiome (VMB), allowing for a better understanding of all potential etiologies. Here, we describe a robust VMB metagenomics sequencing test with a sensitivity of 93.1%, a specificity of 90%, a negative predictive value of 93.4%, and a positive predictive value of 89.6% certified by Clinical Laboratory Improvement Amendments (CLIA), the College of American Pathologist (CAP), and the Clinical Laboratory Evaluation Program (CLEP). We sequenced over 7000 human vaginal samples with this pipeline and described general findings and comparisons to US census data.},
}
@article {pmid39335298,
year = {2024},
author = {Tang, J and Wang, Q and Yu, H and Dong, L and Tang, M and Arif, A and Zhang, G and Zhang, T and Xie, K and Su, S and Zhao, Z and Dai, G},
title = {A Comparison of the Cecal Microbiota between the Infection and Recovery Periods in Chickens with Different Susceptibilities to Eimeria tenella.},
journal = {Animals : an open access journal from MDPI},
volume = {14},
number = {18},
pages = {},
doi = {10.3390/ani14182709},
pmid = {39335298},
issn = {2076-2615},
support = {JATS [2023]447//the Jiangsu Agricultural Industry Technology System/ ; },
abstract = {To investigate the effect of Eimeria tenella (E. tenella) infection on the cecal microbiota, resistant and susceptible families were screened out based on the coccidiosis resistance evaluation indexes after E. tenella infection. Subsequently, a comparative analysis of cecal microorganisms among control, resistant, and susceptible groups as well as between different periods following the E. tenella challenge was conducted using metagenomic sequencing technology. The results showed that the abundance of opportunistic pathogens, such as Pantoea, Sporomusa, and Pasteurella in the susceptible group and Helicobacter and Sutterella in the resistant group, was significantly higher on day 27 post-inoculation (PI) (the recovery period) than on day 5 PI (the infection period). Additionally, the abundance of Alistipes, Butyricicoccus, and Eubacterium in the susceptible group and Coprococcus, Roseburia, Butyricicoccus, and Lactobacillus in the resistant group showed a significant upward trend during the infection period compared with that in the recovery period. On day 5 PI, the abundance of Faecalibacterium and Lactobacillus was decreased in both the resistant and susceptible groups when compared with that in the control group and was greater in the resistant group than in the susceptible group, while Alistipes in the susceptible group had a relatively higher abundance than that in other groups. A total of 49 biomarker taxa were identified using the linear discriminant analysis (LDA) effect size (LEfSe) method. Of these, the relative abundance of Lactobacillus aviarius, Lactobacillus salivarius, Roseburia, and Ruminococcus gauvreauii was increased in the resistant group, while Bacteroides_sp__AGMB03916, Fusobacterium_mortiferum, Alistipes_sp__An31A, and Alistipes_sp__Marseille_P5061 were enriched in the susceptible group. On day 27 PI, LDA scores identified 43 biomarkers, among which the relative abundance of Elusimicrobium_sp__An273 and Desulfovibrio_sp__An276 was increased in the resistant group, while that of Bacteroides_sp__43_108, Chlamydiia, Chlamydiales, and Sutterella_sp__AM11 39 was augmented in the susceptible group. Our results indicated that E. tenella infection affects the structure of the cecal microbiota during both the challenge and recovery periods. These findings will enhance the understanding of the effects of changes in the cecal microbiota on chickens after coccidia infection and provide a reference for further research on the mechanisms underlying how the intestinal microbiota influence the growth and health of chickens.},
}
@article {pmid39335279,
year = {2024},
author = {Cheng, Z and Huang, H and Qiao, G and Wang, Y and Wang, X and Yue, Y and Gao, Q and Peng, S},
title = {Metagenomic and Metabolomic Analyses Reveal the Role of Gut Microbiome-Associated Metabolites in the Muscle Elasticity of the Large Yellow Croaker (Larimichthys crocea).},
journal = {Animals : an open access journal from MDPI},
volume = {14},
number = {18},
pages = {},
doi = {10.3390/ani14182690},
pmid = {39335279},
issn = {2076-2615},
support = {2021Z01//the Central Nonprofit Basic Scientific Research Project for the Scientific Research Institutes of China/ ; 2022YFD2401004//This work was supported by a grant from the National&#xa0;Key&#xa0;Research and&#xa0;Development&#xa0;Program&#xa0;of China/ ; },
abstract = {The large yellow croaker (LYC, Larimichthys crocea) is highly regarded for its delicious taste and unique flavor. The gut microbiota has the ability to affect the host muscle performance and elasticity by regulating nutrient metabolism. The purpose of this study is to establish the relationship between muscle quality and intestinal flora in order to provide reference for the improvement of the muscle elasticity of LYC. In this study, the intestinal contents of high muscle elasticity males (IEHM), females (IEHF), and low muscle elasticity males (IELM) and females (IELF) were collected and subjected to metagenomic and metabolomic analyses. Metagenomic sequencing results showed that the intestinal flora structures of LYCs with different muscle elasticities were significantly different. The abundance of Streptophyta in the IELM (24.63%) and IELF (29.68%) groups was significantly higher than that in the IEHM and IEHF groups. The abundance of Vibrio scophthalmi (66.66%) in the IEHF group was the highest. Based on metabolomic analysis by liquid chromatograph-mass spectrometry, 107 differentially abundant metabolites were identified between the IEHM and IELM groups, and 100 differentially abundant metabolites were identified between the IEHF and IELF groups. Based on these metabolites, a large number of enriched metabolic pathways related to muscle elasticity were identified. Significant differences in the intestinal metabolism between groups with different muscle elasticities were identified. Moreover, the model of the relationship between the intestinal flora and metabolites was constructed, and the molecular mechanism of intestinal flora regulation of the nutrient metabolism was further revealed. The results help to understand the molecular mechanism of different muscle elasticities of LYC and provide an important reference for the study of the mechanism of the effects of LYC intestinal symbiotic bacteria on muscle development, and the development and application of probiotics in LYC.},
}
@article {pmid39334245,
year = {2024},
author = {Van Herzele, C and Coppens, S and Vereecke, N and Theuns, S and de Graaf, DC and Nauwynck, H},
title = {New insights into honey bee viral and bacterial seasonal infection patterns using third-generation nanopore sequencing on honey bee haemolymph.},
journal = {Veterinary research},
volume = {55},
number = {1},
pages = {118},
pmid = {39334245},
issn = {1297-9716},
support = {1SB3123N//Fonds Wetenschappelijk Onderzoek/ ; Baekeland mandate HBC.2020.2889//Agentschap Innoveren en Ondernemen/ ; },
mesh = {Animals ; Bees/virology/microbiology ; *Seasons ; *Hemolymph/virology/microbiology ; Nanopore Sequencing/methods/veterinary ; Bacteria/genetics/isolation &amp; purification/classification ; Virome ; },
abstract = {Honey bees are rapidly declining, which poses a significant threat to our environment and agriculture industry. These vital insects face a disease complex believed to be caused by a combination of parasites, viruses, pesticides, and nutritional deficiencies. However, the real aetiology is still enigmatic. Due to the conventional analysis methods, we still lack complete insights into the honey bee virome and the presence of pathogenic bacteria. To fill this knowledge gap, we employed third-generation nanopore metagenomic sequencing on honey bee haemolymph to monitor the presence of pathogens over almost a year. This study provides valuable insights into the changes in bacterial and viral loads within honey bee colonies. We identified different pathogens in the honey bee haemolymph, which are not included in honey bee screenings. These pathogens comprise the Apis mellifera filamentous virus, Apis rhabdoviruses, and various bacteria such as Frischella sp. and Arsenophonus sp. Furthermore, a sharp contrast was observed between young and old bees. Our research proposes that transgenerational immune priming may play a role in shaping infection patterns in honey bees. We observed a significant increase in pathogen loads in the spring, followed by a notable decrease in pathogen presence during the summer and autumn months. However, certain pathogens seem to be able to evade this priming effect, making them particularly intriguing as potential factors contributing to mortality. In the future, we aim to expand our research on honey bee transgenerational immune priming and investigate its potential in natural settings. This knowledge will ultimately enhance honey bee health and decrease colony mortality.},
}
@article {pmid39334144,
year = {2024},
author = {Foro Ramos, EDS and da Silva Couto, R and Tozetto-Mendoza, TR and Bortoletto, P and Barbosa, EMG and Ferreira, NE and Linhares, IM and Spandorfer, SD and da Costa, AC and Leal, E and Mendes-Correa, MC and Witkin, SS},
title = {Characterization of multiple human papillomavirus types in the human vagina following ovarian hormonal stimulation.},
journal = {Virology journal},
volume = {21},
number = {1},
pages = {229},
pmid = {39334144},
issn = {1743-422X},
support = {CAPES//scholarship provided by the Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior-Brasil/ ; CAPES//scholarship provided by the Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior-Brasil/ ; HCFMUSP//scholarship from HCFMUSP with funds donated by NUBANK under the #HCCOMVIDA scheme/ ; },
mesh = {Humans ; Female ; *Vagina/virology ; *Papillomavirus Infections/virology ; Adult ; *Phylogeny ; *Papillomaviridae/genetics/classification/isolation &amp; purification ; *Ovulation Induction ; DNA, Viral/genetics ; Sequence Analysis, DNA ; Young Adult ; Metagenomics ; Genotype ; Human Papillomavirus Viruses ; },
abstract = {The objective of study was to characterize HPV in vaginal samples from women being seen at the Center for Reproductive Medicine and Infertility at Weill Cornell Medicine before and following ovarian stimulation. A total of 29 women made samples available for analysis by viral metagenomics. Eighteen women were HPV-positive, six (33.3%) at their initial visit and 15 (83.3%) following hormone stimulation (p = 0.0059). Pairwise comparison of nucleotide sequences and phylogenetic analysis showed the classification sequences into two genera: Alphapapillomavirus and Gammapapillomavirus. Sequences were from 8 HPV types: HPV 51 (n = 2), HPV 68 (n = 1), HPV 83 (n = 9), HPV 84 (n = 2), HPV 121 (n = 6), HPV 175 (n = 1) and HPV 190 (n = 1). Additionally, C16b and C30 likely represent new types. In summary, multiple HPV types are present in the vagina of reproductive age women and are induced by hormone used to stimulate ovulation.},
}
@article {pmid39334057,
year = {2024},
author = {Wang, C and Hu, ZW and Li, ZY and Zhao, MH and Little, MA and Chen, M},
title = {Advantages of metagenomic next-generation sequencing in the management of ANCA-associated vasculitis patients with suspected pulmonary infection as a rule-out tool.},
journal = {BMC pulmonary medicine},
volume = {24},
number = {1},
pages = {478},
pmid = {39334057},
issn = {1471-2466},
support = {BJPSTP-2024-15//Beijing Physician Scientist Training Project/ ; BMU2024PYJH009//Peking University Clinical Scientist Training Program, supported by "the Fundamental Research Funds for the Central Universities"/ ; 2022YFC2502500/2022YFC2502502//National Key Research and Development Program of China/ ; 2022YFC2502500/2022YFC2502502//National Key Research and Development Program of China/ ; 82090020/82090021 and 82270754//National Natural Science Fund/ ; 82090020/82090021 and 82270754//National Natural Science Fund/ ; 2019RU023//Chinese Academy of Medical Sciences Research Unit/ ; 2019RU023//Chinese Academy of Medical Sciences Research Unit/ ; 2022CR52//National High Level Hospital Clinical Research Funding (Multi-center Clinical Research Project of Peking University First Hospital)/ ; 2022CR52//National High Level Hospital Clinical Research Funding (Multi-center Clinical Research Project of Peking University First Hospital)/ ; 2024HQ01//National High Level Hospital Clinical Research Funding (High Quality Clinical Research Project of Peking University First Hospital)/ ; 2024HQ01//National High Level Hospital Clinical Research Funding (High Quality Clinical Research Project of Peking University First Hospital)/ ; },
mesh = {Humans ; *Anti-Neutrophil Cytoplasmic Antibody-Associated Vasculitis/diagnosis/drug therapy ; Male ; Female ; Middle Aged ; *Bronchoalveolar Lavage Fluid/microbiology ; Retrospective Studies ; Aged ; *High-Throughput Nucleotide Sequencing ; *Metagenomics/methods ; Bronchoscopy ; Hospital Mortality ; Respiratory Tract Infections/microbiology/diagnosis/drug therapy ; Adult ; },
abstract = {OBJECTIVE: Pulmonary infection is one of the leading causes of death in patients with ANCA-associated vasculitis (AAV). It is sometimes difficult to differentiate pulmonary infection from pulmonary involvement of vasculitis in AAV patients. Fiberoptic bronchoscopy and bronchoalveolar lavage fluid (BALF) assays are useful diagnostic methods. In addition to conventional microbiological tests (CMTs), metagenomic next-generation sequencing (mNGS) facilitates rapid and sensitive detection of various pathogens. The current study aimed to evaluate the advantages of additional BALF mNGS in the management of pulmonary infection in AAV patients.<br><br>METHODS: 27 patients with active AAV and suspected pulmonary infection whose BALF samples were tested by mNGS and CMTs and 17 active AAV patients whose BALF were tested by CMTs alone were retrospectively recruited. The results of microbiological tests, and adjustments of treatment following BALF mNGS, were described. The durations of antimicrobial treatment and in-hospital mortality in patients were compared.<br><br>RESULTS: Among the 27 patients whose BALF samples were tested by mNGS, 25.9% of patients did not have evidence of pathogenic microorganism in their BALF samples, 55.6% had polymicrobial infections, including bacteria, fungi and viruses. Of these 27 patients, 40.7% did not have evidence of pathogenic microorganism in their BALF or serum samples according to CMTs. Patients in the BALF mNGS/CMT group received a significantly shorter duration of antibacterial and total antimicrobial treatment than patients in the CMT alone group (17.3&#x2009;&#xb1;&#x2009;14.7 vs. 27.9&#x2009;&#xb1;&#x2009;19.0 days, P&#x2009;=&#x2009;0.044; 18.9&#x2009;&#xb1;&#x2009;15.0 vs. 29.5&#x2009;&#xb1;&#x2009;17.7 days, P&#x2009;=&#x2009;0.040, respectively). Fewer patients in the BALF mNGS/CMT group died than in the CMT alone group (4/27 vs. 7/17, P&#x2009;=&#x2009;0.049).<br><br>CONCLUSION: Compared with CMT alone, additional mNGS tests may shorten the duration of antimicrobial treatment and possibly decrease death from severe infection by providing precise and quick diagnosis of infection.},
}
@article {pmid39333982,
year = {2024},
author = {Kanagiri, T and Meena, DS and Kumar, D and Midha, NK and Kombade, S and Yadav, T},
title = {Recurrent pulmonary nocardiosis due to Nocardia Otitidiscaviarum in a patient with isolated CD4 lymphocytopenia: a case report.},
journal = {BMC infectious diseases},
volume = {24},
number = {1},
pages = {1033},
pmid = {39333982},
issn = {1471-2334},
mesh = {Humans ; Female ; *Nocardia Infections/drug therapy/microbiology/diagnosis ; Middle Aged ; *Nocardia/isolation &amp; purification/genetics ; Recurrence ; T-Lymphocytopenia, Idiopathic CD4-Positive/complications ; Anti-Bacterial Agents/therapeutic use ; Trimethoprim, Sulfamethoxazole Drug Combination/therapeutic use ; CD4 Lymphocyte Count ; Lymphopenia/complications ; },
abstract = {BACKGROUND: Idiopathic CD4 lymphocytopenia (ICL) is an underdiagnosed immunodeficiency syndrome characterised by persistent low CD4 counts in the absence of HIV and other causes of lymphocytopenia. ICL patients are susceptible to opportunistic infections, with human papillomavirus, cryptococcal, and tuberculosis being the most common infections reported. Nocardiosis is rarely reported in patient with ICL.<br><br>CASE PRESENTATION: We herein discuss a 46-year-old female presented with complaints of weight loss, low grade fever and cough with expectoration from last four months. The patient was diagnosed with pulmonary nocardiosis and aspergillosis co-infection four years back; in addition she also had ICL. Subsequently, the patient was lost in follow-up and readmitted four years later. Bronchoalveolar lavage sample shows the presence of acid-fast bacilli in modified gram stain, which later identified as Nocardia otitidiscaviarum by metagenomic next-generation sequencing. Her CD4 counts were still found low (298 cells/mm[3]). After an initial improvement with trimethoprim-sulfamethoxazole (TMP-SMX), she was commenced on indefinite secondary prophylaxis.<br><br>CONCLUSIONS: Nocardiosis without usual risk factors should be evaluated for ICL. This case emphasize the importance of periodic follow-up with CD4 count monitoring and secondary prophylaxis therapy to prevent recurrence or the emergence of new infections in ICL.<br><br>CLINICAL TRIAL NUMBER: Not applicable.},
}
@article {pmid39333956,
year = {2024},
author = {Ai, L and Qi, Y and Hu, Y and Zhu, C and Liu, K and Li, F and Ye, F and Dai, H and Wu, Y and Kuai, Q and Nie, D and Shan, L and Zhang, Y and Wang, C and Tan, W},
title = {The epidemiological and infectious characteristics of novel types of Coxiella burnetii co-infected with Coxiella-like microorganisms from Xuyi County, Jiangsu province, China.},
journal = {BMC infectious diseases},
volume = {24},
number = {1},
pages = {1041},
pmid = {39333956},
issn = {1471-2334},
support = {2024YQZL02//Incubation Project of Huadong Research Institute for Medicine and Biotechniques/ ; H2019015, M2020087//Project of Medical Research Topics of Jiangsu Provincial Health Planning Commission/ ; H2019015, M2020087//Project of Medical Research Topics of Jiangsu Provincial Health Planning Commission/ ; BK20221196, BE2022682//Jiangsu Science and Technology Plan/ ; BK20221196, BE2022682//Jiangsu Science and Technology Plan/ ; U1602223//National Natural Science Foundation of China/ ; },
mesh = {*Q Fever/epidemiology/microbiology ; *Coxiella burnetii/genetics/isolation &amp; purification ; Animals ; China/epidemiology ; Humans ; *Ticks/microbiology ; *Hedgehogs/microbiology ; Mice ; Coinfection/microbiology/epidemiology ; Female ; Male ; Seroepidemiologic Studies ; Genotype ; Antibodies, Bacterial/blood ; High-Throughput Nucleotide Sequencing ; Zoonoses/microbiology/epidemiology ; Coxiella/genetics/isolation &amp; purification ; Molecular Epidemiology ; Phylogeny ; },
abstract = {Coxiella burnetii (C. burnetii) is the causative agent of Q fever, a type of zoonoses withwidespread distribution. In 2019, a case of Q fever was diagnosed by metagenomic next-generation sequencing (mNGS) method in Xuyi County (Jiangsu province, China). The seroprevalence of previous fever patients and the molecular epidemiology of Coxiella in wild hedgehogs and harbouring ticks around the confirmed patient were detected to reveal the genetic characteristics and pathogenicity of the Coxiella strains. Four of the 90 serum samples (4.44%) were positive for specific C. burnetii IgM antibody, suggesting that local humans are at risk of Q fever. The positive rates of C. burnetii in hedgehogs and ticks were 21.9% (7/32) and 70.5% (122/173), respectively. At least 3 strains of Coxiella were found prevalent in the investigated area, including one new genotype of pathogenic C. burnetii (XYHT29) and two non-pathogenic Coxiella-like organisms (XYHT19 and XYHT3). XYHT29 carried by ticks and wild hedgehogs successfully infected mice, imposing a potential threat to local humans. XYHT19, a novel Coxiella-like microorganism, was first discovered in the world to co-infect with C. burnetii in Haemaphysalis flava. The study provided significant epidemic information that could be used for prevention and control strategies against Q fever for local public health departments and medical institutions.},
}
@article {pmid39333778,
year = {2024},
author = {Msango, K and Gouda, MNR and Ramakrishnan, B and Kumar, A and Subramanian, S},
title = {Variation and functional profile of gut bacteria in the scarab beetle, Anomala dimidiata, under a cellulose-enriched microenvironment.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {22400},
pmid = {39333778},
issn = {2045-2322},
mesh = {Animals ; *Coleoptera/microbiology ; *Cellulose/metabolism ; *Gastrointestinal Microbiome ; *Bacteria/genetics/metabolism/classification/isolation &amp; purification ; Larva/microbiology ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Symbiosis ; },
abstract = {This study utilized cultivable methods and 16 S amplicon sequencing to compare taxonomic profiles and functional potential of gut bacteria in the scarab beetle, Anomola dimidiata, under cellulose-enriched conditions. Eight culturable cellulolytic gut bacteria were isolated from the midgut and hindgut of the scarab larvae, respectively. 16 S amplicon sequencing evinced that the most represented taxonomic profiles at phylum level in the fermentation chamber and midgut were Bacillota (71.62 and 56.76%), Pseudomonadota (22.66 and 36.89%) and Bacteroidota (2.7 and 2.81%). Bacillota (56.74 and 91.39%) were significantly enriched in the midgut with the addition of cellulose. In contrast, Bacillota and Psedomonadota were significantly enriched in the fermentation chamber. Carbohydrate metabolism was up-regulated in the midgut, while nitrogen and phosphorus metabolism were up-regulated in the fermentation chamber, suggesting these symbionts' possible metabolic roles to the host. An analysis of total cellulases as well as amplicon sequence variants indicated that the gut bacteria belonging to Acinetobacter, Bacillus, Brucella, Brevibacillus, Enterobacter, Lysinibacillus and Paenibacillus are involved in nutrition provisioning. These results have provided additional insights into the gut bacteria associated with cellulose digestion in A. dimidiata and created a platform for bioprospecting novel isolates to produce biomolecules for biotechnological use, besides identifying eco-friendly targets for its management.},
}
@article {pmid39333734,
year = {2024},
author = {Ishak, S and Rondeau-Leclaire, J and Faticov, M and Roy, S and Laforest-Lapointe, I},
title = {Boreal moss-microbe interactions are revealed through metagenome assembly of novel bacterial species.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {22168},
pmid = {39333734},
issn = {2045-2322},
mesh = {*Bryophyta/microbiology ; *Bacteria/genetics/metabolism/classification ; *Metagenome ; Taiga ; Metagenomics/methods ; Microbiota ; Quebec ; Nitrogen Fixation ; Photosynthesis ; },
abstract = {Moss-microbe interactions contribute to ecosystem processes in boreal forests. Yet, how host-specific characteristics and the environment drive the composition and metabolic potential of moss microbiomes is still poorly understood. In this study, we use shotgun metagenomics to identify the taxonomy and metabolic potential of the bacteria of four moss species of the boreal forests of Northern Québec, Canada. To characterize moss bacterial community composition and diversity, we assembled the genomes of 110 potentially novel bacterial species. Our results highlight that moss genus, species, gametophyte section, and to a lesser extent soil pH and soil temperature, drive moss-associated bacterial community composition and diversity. In the brown gametophyte section, two Stigonema spp. showed partial pathway completeness for photosynthesis and nitrogen fixation, while all brown-associated Hyphomicrobiales had complete assimilatory nitrate reduction pathways and many nearly complete carbon fixation pathways. Several brown-associated species showed partial to complete pathways for coenzyme M and F420 biosynthesis, important for methane metabolism. In addition, green-associated Hyphomicrobiales (Methylobacteria spp.) displayed potential for the anoxygenic photosystem II pathway. Overall, our findings demonstrate how host-specific characteristics and environmental factors shape the composition and metabolic potential of moss bacteria, highlighting their roles in carbon fixation, nitrogen cycling, and methane metabolism in boreal forests.},
}
@article {pmid39333577,
year = {2024},
author = {Zhao, B and Zi, M and Zhang, X and Wang, Y},
title = {Microbial communities and metagenomes in methane-rich deep coastal sediments.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {1043},
pmid = {39333577},
issn = {2052-4463},
support = {U22B2012//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Methane/metabolism ; *Geologic Sediments/microbiology ; *Microbiota ; *Metagenome ; *Archaea/genetics ; *RNA, Ribosomal, 16S/genetics ; Phylogeny ; },
abstract = {Coastal sediments are rich in embedded recalcitrant organic carbons that are biotransformed into methane. In this study, gas composition (carbon dioxide, methane and nitrogen) and chemical indicators (total nitrogen, total carbon, and total sulfate) were examined in five deep sediment cores (up to 130 m in length) obtained from the Hangzhou Bay. The V3-V4 region of the 16S rRNA gene amplicons was amplified and sequenced for the prokaryotic community analysis. The species composition, along with the physicochemical factors of the sediments, revealed a strong correlation with methane content in one of the sediment cores. We then obtained metagenomes of the two sediment samples selected for their high methane content and enrichment of methanogenic Bathyarchaeota with phylogenetic evidence. A total of 27 draft genomes were retrieved through metagenomic binning methodologies and were classified into Bathyarchaeota, Asgard archaea, Planctomycetes, and other microbial groups. The data provided are valuable for understanding the relationship between methane generation and microbial community composition in deep sediment core samples from coastal to marine environments.},
}
@article {pmid39333527,
year = {2024},
author = {Cheng, M and Xu, Y and Cui, X and Wei, X and Chang, Y and Xu, J and Lei, C and Xue, L and Zheng, Y and Wang, Z and Huang, L and Zheng, M and Luo, H and Leng, Y and Jiang, C},
title = {Deep longitudinal lower respiratory tract microbiome profiling reveals genome-resolved functional and evolutionary dynamics in critical illness.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {8361},
pmid = {39333527},
issn = {2041-1723},
mesh = {Humans ; *Critical Illness ; *Microbiota/genetics ; *Intensive Care Units ; *Metagenome/genetics ; Metagenomics/methods ; Longitudinal Studies ; Male ; Female ; Plasmids/genetics ; Genome, Bacterial/genetics ; Respiratory System/microbiology ; Aged ; Middle Aged ; Bacteria/genetics/classification/isolation &amp; purification ; Pneumonia/microbiology ; Evolution, Molecular ; },
abstract = {The lower respiratory tract (LRT) microbiome impacts human health, especially among critically ill patients. However, comprehensive characterizations of the LRT microbiome remain challenging due to low microbial mass and host contamination. We develop a chelex100-based low-biomass microbial-enrichment method (CMEM) that enables deep metagenomic profiling of LRT samples to recover near-complete microbial genomes. We apply the method to 453 longitudinal LRT samples from 157 intensive care unit (ICU) patients in three geographically distant hospitals. We recover 120 high-quality metagenome-assembled genomes (MAGs) and associated plasmids without culturing. We detect divergent longitudinal microbiome dynamics and hospital-specific dominant opportunistic pathogens and resistomes in pneumonia patients. Diagnosed pneumonia and the ICU stay duration were associated with the abundance of specific antibiotic-resistance genes (ARGs). Moreover, CMEM can serve as a robust tool for genome-resolved analyses. MAG-based analyses reveal strain-specific resistome and virulome among opportunistic pathogen strains. Evolutionary analyses discover increased mobilome in prevailing opportunistic pathogens, highly conserved plasmids, and new recombination hotspots associated with conjugative elements and prophages. Integrative analysis with epidemiological data reveals frequent putative inter-patient strain transmissions in ICUs. In summary, we present a genome-resolved functional, transmission, and evolutionary landscape of the LRT microbiota in critically ill patients.},
}
@article {pmid39333501,
year = {2024},
author = {Kutuzova, S and Nielsen, M and Piera, P and Nissen, JN and Rasmussen, S},
title = {Taxometer: Improving taxonomic classification of metagenomics contigs.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {8357},
pmid = {39333501},
issn = {2041-1723},
support = {NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF14CC0001//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF21SA0072102//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; },
abstract = {For taxonomy based classification of metagenomics assembled contigs, current methods use sequence similarity to identify their most likely taxonomy. However, in the related field of metagenomic binning, contigs are routinely clustered using information from both the contig sequences and their abundance. We introduce Taxometer, a neural network based method that improves the annotations and estimates the quality of any taxonomic classifier using contig abundance profiles and tetra-nucleotide frequencies. We apply Taxometer to five short-read CAMI2 datasets and find that it increases the average share of correct species-level contig annotations of the MMSeqs2 tool from 66.6% to 86.2%. Additionally, it reduce the share of wrong species-level annotations in the CAMI2 Rhizosphere dataset by an average of two-fold for Metabuli, Centrifuge, and Kraken2. Futhermore, we use Taxometer for benchmarking taxonomic classifiers on two complex long-read metagenomics data sets where ground truth is not known. Taxometer is available as open-source software and can enhance any taxonomic annotation of metagenomic contigs.},
}
@article {pmid39333274,
year = {2024},
author = {Licheri, M and Licheri, MF and Probst, L and Sägesser, C and Bittel, P and Suter-Riniker, F and Dijkman, R},
title = {A novel isothermal whole genome sequencing approach for Monkeypox Virus.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {22333},
pmid = {39333274},
issn = {2045-2322},
mesh = {*Whole Genome Sequencing/methods ; Humans ; *Genome, Viral ; *Monkeypox virus/genetics ; Mpox (monkeypox)/virology/epidemiology ; DNA, Viral/genetics ; Nucleic Acid Amplification Techniques/methods ; Disease Outbreaks ; Animals ; },
abstract = {Monkeypox virus (MPXV) is the zoonotic agent responsible for mpox, an often-self-limiting pox-like disease. Since May 2022, an outbreak characterized by increased human-to-human transmission was detected outside the endemic regions. Whole genome sequencing (WGS) has been successfully used to keep track of viral evolution during outbreaks or for surveillance of multiple pathogens of public health significance. Current WGS protocols for MPXV are either based on metagenomic sequencing or tiled-PCR amplification. The latter allows multiplexing due to the efficient enrichment of the viral DNA, however, mutations or the presence of different clades can negatively influence genome coverage yield. Here, we present the establishment of a novel isothermal WGS method for MPXV based on Phi29 DNA polymerase-based multiple displacement amplification (MDA) properties making use of only 6 primers. This approach yielded from 88% up to 100% genome coverage using either alkaline denatured extracted DNA or clinical material as starting material, with the highest coverage generated by clinical material. We demonstrate that this novel isothermal WGS protocol is suitable for monitoring viral evolution during MPXV outbreaks and surveillance in any conventional laboratory setting.},
}
@article {pmid39333204,
year = {2024},
author = {Martin Říhová, J and Gupta, S and Nováková, E and Hypša, V},
title = {Fur microbiome as a putative source of symbiotic bacteria in sucking lice.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {22326},
pmid = {39333204},
issn = {2045-2322},
support = {GA20-07674S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; },
mesh = {Animals ; *Symbiosis ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Phthiraptera/microbiology ; Bacteria/genetics/classification/isolation &amp; purification ; },
abstract = {Symbiosis between insects and bacteria has been established countless times. While it is well known that the symbionts originated from a variety of different bacterial taxa, it is usually difficult to determine their environmental source and a route of their acquisition by the host. In this study, we address this question using a model of Neisseriaceae symbionts in rodent lice. These bacteria established their symbiosis independently with different louse taxa (Polyplax, Hoplopleura, Neohaematopinus), most likely from the same environmental source. We first applied amplicon analysis to screen for candidate source bacterium in the louse environment. Since lice are permanent ectoparasites, often specific to the particular host, we screened various microbiomes associated with three rodent species (Microtus arvalis, Clethrionomys glareolus, and Apodemus flavicollis). The analyzed samples included fur, skin, spleen, and other ectoparasites sampled from these rodents. The fur microbiome data revealed a Neisseriaceae bacterium, closely related to the known louse symbionts. The draft genomes of the environmental Neisseriaceae, assembled from all three rodent hosts, converged to a remarkably small size of approximately 1.4 Mbp, being even smaller than the genomes of the related symbionts. Our results suggest that the rodent fur microbiome can serve as a source for independent establishment of bacterial symbiosis in associated louse species. We further propose a hypothetical scenario of the genome evolution during the transition of a free-living bacterium to the member of the rodent fur-associated microbiome and subsequently to the facultative and obligate louse symbionts.},
}
@article {pmid39333145,
year = {2024},
author = {Boie, W and Schemmel, M and Ye, W and Hasler, M and Goll, M and Verreet, JA and Cai, D},
title = {An assessment of the species diversity and disease potential of Pythium communities in Europe.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {8369},
pmid = {39333145},
issn = {2041-1723},
support = {031B0910-A//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; 221NR-058B//Fachagentur Nachwachsende Rohstoffe (Agency for Renewable Resources)/ ; },
mesh = {*Pythium/genetics/isolation &amp; purification ; Europe ; *Plant Diseases/microbiology ; *Zea mays/microbiology ; Soil Microbiology ; Biodiversity ; Metagenomics/methods ; },
abstract = {Pythium sensu lato (s.l.) is a genus of parasitic oomycetes that poses a serious threat to agricultural production worldwide, but their severity is often neglected because little knowledge about them is available. Using an internal transcribed spacer (ITS) amplicon-based-metagenomics approach, we investigate the occurrence, abundance, and diversity of Pythium spp. s.l. in 127 corn fields of 11 European countries from the years 2019 to 2021. We also identify 73 species, with up to 20 species in a single soil sample, and the prevalent species, which show high species diversity, varying disease potential, and are widespread in most countries. Further, we show species-species co-occurrence patterns considering all detected species and link species abundance to soil parameter using the LUCAS topsoil dataset. Infection experiments with recovered isolates show that Pythium s.l. differ in disease potential, and that effective interference with plant hormone networks suppressing JA (jasmonate)-mediated defenses is an essential component of the virulence mechanism of Pythium s.l. species. This study provides a valuable dataset that enables deep insights into the structure and species diversity of Pythium s.l. communities in European corn fields and knowledge for better understanding plant-Pythium interactions, facilitating the development of an effective strategy to cope with this pathogen.},
}
@article {pmid39333115,
year = {2024},
author = {Liao, H and Liu, C and Zhou, S and Liu, C and Eldridge, DJ and Ai, C and Wilhelm, SW and Singh, BK and Liang, X and Radosevich, M and Yang, QE and Tang, X and Wei, Z and Friman, VP and Gillings, M and Delgado-Baquerizo, M and Zhu, YG},
title = {Prophage-encoded antibiotic resistance genes are enriched in human-impacted environments.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {8315},
pmid = {39333115},
issn = {2041-1723},
mesh = {*Prophages/genetics ; Humans ; *Drug Resistance, Bacterial/genetics ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/virology/drug effects ; Genome, Bacterial/genetics ; Metagenome/genetics ; Ecosystem ; Escherichia coli/genetics/virology/drug effects ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; },
abstract = {The spread of antibiotic resistance genes (ARGs) poses a substantial threat to human health. Phage-mediated transduction could exacerbate ARG transmission. While several case studies exist, it is yet unclear to what extent phages encode and mobilize ARGs at the global scale and whether human impacts play a role in this across different habitats. Here, we combine 38,605 bacterial genomes, 1432 metagenomes, and 1186 metatranscriptomes across 12 contrasting habitats to explore the distribution of prophages and their cargo ARGs in natural and human-impacted environments. Worldwide, we observe a significant increase in the abundance, diversity, and activity of prophage-encoded ARGs in human-impacted habitats linked with relatively higher risk of past antibiotic exposure. This effect was driven by phage-encoded cargo ARGs that could be mobilized to provide increased resistance in heterologous E. coli host for a subset of analyzed strains. Our findings suggest that human activities have altered bacteria-phage interactions, enriching ARGs in prophages and making ARGs more mobile across habitats globally.},
}
@article {pmid39333059,
year = {2024},
author = {Lin, W and Li, R and Cao, S and Li, H and Yang, K and Yang, Z and Su, J and Zhu, YG and Cui, L},
title = {High-Throughput Single-Cell Metabolic Labeling, Sorting, and Sequencing of Active Antibiotic-Resistant Bacteria in the Environment.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c02906},
pmid = {39333059},
issn = {1520-5851},
abstract = {Active antibiotic-resistant bacteria (ARB) play a major role in spreading antimicrobial resistance (AMR) in the environment; however, they have remained largely unexplored. Herein, we coupled bio-orthogonal noncanonical amino acid tagging with high-throughput fluorescence-activated single-cell sorting (FACS) and sequencing to characterize the phenome and genome of active ARB in complex environmental matrices. Active ARB, conferring resistance to six antibiotics throughout wastewater treatment, were distinguished and quantified. The percentage and concentration of active ARB ranged from 0.28% to 45.3% and from 1.1 × 10[4] to 2.09 × 10[7] cells/mL, respectively. Notably, the final effluents retained up to 4.79 × 10[4] cells/mL of active ARB. Targeted FACS and genomic sequencing revealed a distinct taxonomic composition of active ARB compared with that of the overall population. The coexistence of antibiotic resistome and mobilome in active ARB was also identified, including three high-quality metagenomic assembly genomes assigned to pathogenic bacteria, highlighting the substantial health risks due to their activity, phenotypic resistance, mobility, and pathogenicity. This study advances our understanding of previously overlooked active ARB in the environment by linking their resistance phenotype to their genotype. This high-throughput method will enable efficient quantitative surveillance of active AMR, providing valuable insights into risk control and management.},
}
@article {pmid39332981,
year = {2024},
author = {Olsen, M and Goldsworthy, A and Morgan, M and Leggett, J and Demaneuf, T and Van Der Bruggen, N and Singh, G and Ghemrawi, R and Senok, A and Almheiri, R and McKirdy, S and Alghafri, R and Tajouri, L},
title = {Microbial laden mobile phones from international conference attendees pose potential risks to public health and biosecurity.},
journal = {Infection, disease &amp; health},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.idh.2024.08.004},
pmid = {39332981},
issn = {2468-0869},
abstract = {INTRODUCTION: Mobile phones, contaminated with pathogenic microorganisms, have the potential to act as "trojan horses". The microbial signatures present on their surfaces most probably vary across different geographical regions. As a result, mobile phones belonging to international conference attendees may serve as a model for global microbial dissemination, posing potential risks to public health and biosecurity.<br><br>AIM: This study aimed to profile the microbes present on mobile phones belonging to delegates attending an international scientific conference through use of metagenomic shotgun DNA sequencing.<br><br>METHODS: Twenty mobile phones, representing ten different geographical zones from around the world, were swabbed and pooled together into ten geographical-specific samples for high definition next-generation DNA sequencing. WONCA council members were invited to participate and provided verbal consent. Following DNA extraction, next generation sequencing, to a depth of approximately 10Gbp per sample, was undertaken on a v1.5 Illumina NovaSeq6000 system. Bioinformatic analysis was performed via the CosmosID platform.<br><br>RESULTS: A total of 2204 microbial hits were accumulated across 20 mobile phones inclusive of 882 bacteria, 1229 viruses, 88 fungi and 5 protozoa. Of particular concern was the identification of 65 distinct antibiotic resistance genes and 86 virulence genes. Plant, animal and human pathogens, including ESKAPE and HACEK bacteria were found on mobile phones.<br><br>DISCUSSION/CONCLUSION: Mobile phones of international attendees are contaminated with many &amp; varied microorganisms. Further research is required to characterize the risks these devices pose for biosecurity and public health. Development of new policies which appropriately address and prevent such risks maybe warranted.},
}
@article {pmid39332349,
year = {2024},
author = {Sun, Q and Zhang, Z and Ping, Q and Wang, L and Li, Y},
title = {Insight into using multi-omics analysis to elucidate nitrogen removal mechanisms in a novel improved constructed rapid infiltration system: Functional gene and metabolite signatures.},
journal = {Water research},
volume = {267},
number = {},
pages = {122502},
doi = {10.1016/j.watres.2024.122502},
pmid = {39332349},
issn = {1879-2448},
abstract = {In this study, a laboratory-scale improved constructed rapid infiltration (imCRI) system with non-saturated and saturated layers was constructed, and corn cobs as solid carbon source were added to the saturated layer to enhance the removal of nitrogen. Combined analyses of metagenomics and metabolomics were conducted to elucidate the nitrogen removal mechanism in the imCRI system. The results showed that the hydraulic load significantly influenced the treatment performance of the imCRI system, and a hydraulic load of 1.25 m[3]/(m[2]⋅d) was recommended. Under optimal conditions, the imCRI system using simulated wastewater achieved average removal efficiencies of 97.8 % for chemical oxygen demand, 85.7 % for total nitrogen (TN), and 97.6 % for ammonia nitrogen. Metagenomic and metabolomic analyses revealed that besides nitrification and denitrification, dissimilatory nitrate reduction to ammonium (DNRA), anammox, etc., are also involved in nitrogen metabolism in the imCRI system. Although nitrification was the predominant pathway in the non-saturated layer, aerobic denitrification also occurred, accounting for 22.59 % of the TN removal. In the saturated layer, nitrogen removal was attributed to synergistic effects of denitrification, DNRA and anammox. Moreover, correlation analysis among nitrogen removal, functional genes and metabolites suggested that metabolites related to the tricarboxylic acid cycle generated from the glycolysis of corn cobs provided sufficient energy for denitrification. Our results can offer a promising technology for decentralized wastewater treatment with stringent nitrogen removal requirements, and provide a foundation for understanding the underlying nitrogen transformation and removal mechanism.},
}
@article {pmid39332305,
year = {2024},
author = {Zhang, J and Chen, J and Wang, C and Wang, P and Gao, H and Feng, B and Fu, J},
title = {Vertical variation of antibiotic resistance genes and their interaction with environmental nutrients in sediments of Taihu lake.},
journal = {Journal of environmental management},
volume = {370},
number = {},
pages = {122661},
doi = {10.1016/j.jenvman.2024.122661},
pmid = {39332305},
issn = {1095-8630},
abstract = {Antibiotic resistance is a growing environmental issue. As a sink for antibiotic resistance genes (ARGs), lake surface sediments are well known for the spread of ARGs. However, the distribution pattern of ARGs and their relationship with environmental factors in vertical sediment layers are unclear. In this study, we investigated the resistome distribution in sediment cores from Taihu Lake using metagenomic analysis. The results showed that the abundance of total ARGs increased by 153% as the sediment depth rose from 0 to 50 cm, and the ARG Shannon index significantly increased. Among all the ARG types, efflux pump genes (e.g., mexT and mexW) were dominant, especially in 40-50 cm sediment. The variation in ARG with depth described above was related to the changes in bacterial adaptation to environmental gradients. Specifically, sulfate and nitrate concentrations decreased with depth, and random forest analysis showed that they were the main factors affecting the changes in ARG abundance. Environmental factors were also found to indirectly impact the distribution of ARGs by affecting the bacterial community. Potential sulfate-reducing gene/nitrate-reducing gene-ARG co-hosts were annotated through metagenomic assembly. The dominant co-hosts, Curvibacter, and Comamonas, which were enriched in deeper sediments, may have contributed to the enrichment of ARGs in deep sediments. Overall, our findings demonstrated that bacterial-mediated sulfate and nitrate reduction was closely related to sediment resistance, which provided new insights into the control of antibiotic resistance.},
}
@article {pmid39332086,
year = {2024},
author = {Sung, YH and Jeong, WK and Lee, HJ and Suh, JW and Kim, JY and Yoon, YK},
title = {Innovative approach of nanopore-based metagenomic sequencing for rapid identification of bacterial pathogens in joint fluid: A pilot study.},
journal = {Diagnostic microbiology and infectious disease},
volume = {110},
number = {4},
pages = {116545},
doi = {10.1016/j.diagmicrobio.2024.116545},
pmid = {39332086},
issn = {1879-0070},
abstract = {Analysis of 11 clinical samples of joint fluid in this pilot study demonstrated proof-of-concept for nanopore-based metagenomic sequencing to serve as a complementary real-time diagnostic technique for septic arthritis, with a sensitivity of 75.0 % and specificity of 57.1 %, compared to the gold standard method of bacterial culture.},
}
@article {pmid39331873,
year = {2024},
author = {Wang, L and Zhang, L and Ying, C and Jin, X and Ying, M and Chen, H and Zhu, D},
title = {Cryptogenic organizing pneumonia caused by solanine: A case report.},
journal = {Medicine},
volume = {103},
number = {39},
pages = {e39807},
doi = {10.1097/MD.0000000000039807},
pmid = {39331873},
issn = {1536-5964},
mesh = {Humans ; Male ; Adult ; *Cryptogenic Organizing Pneumonia/diagnosis/drug therapy/chemically induced ; Glucocorticoids/therapeutic use ; Tomography, X-Ray Computed ; Oxygen Inhalation Therapy ; },
abstract = {RATIONALE: Cryptogenic organizing pneumonia (COP) is a type of pneumonia with unknown cause, presenting with symptoms like dyspnea, fever, and cough. Solanine poisoning can cause symptoms like increased heart rate, rapid breathing, sore throat, diarrhea, vomiting, and fever, but there are no known cases of it causing COP.<br><br>PATIENT CONCERNS: A 43-year-old man had a dry cough, worse at night, with phlegm and chest tightness after eating sprouted potatoes. No history of surgeries or family medical issues.<br><br>DIAGNOSIS: Laboratory tests and metagenomic next-generation sequencing of bronchoalveolar lavage fluid from the bilateral lower lobes did not yield a definitive pathogen. Further evaluation included testing for vasculitis-associated antibodies and rheumatologic immune markers for myositis spectra to rule out connective tissue disease-associated interstitial lung disease as the etiology of organizing pneumonia. As a result, the final diagnosis was determined to be COP.<br><br>INTERVENTIONS: The patient received glucocorticoid therapy and oxygen therapy, and responded well to the treatment.<br><br>OUTCOMES: On the 10th day of hospitalization, the patient was discharged with success. A follow-up chest CT conducted over a month later revealed that the lesions in both lungs had essentially resolved, with only minor residual fibrotic changes present.<br><br>LESSONS: Regularly monitoring disease progression is crucial for patients with solanine poisoning who have pulmonary symptoms. Promptly conducting chest CT scans and bronchoscopy is advised to check for any infections. It is also important to rule out pneumonia related to connective tissue disease-associated interstitial lung disease and provide appropriate treatment promptly.},
}
@article {pmid39327429,
year = {2024},
author = {Schmartz, GP and Rehner, J and Schuff, MJ and Molano, LG and Becker, SL and Krawczyk, M and Tagirdzhanov, A and Gurevich, A and Francke, R and Müller, R and Keller, V and Keller, A},
title = {Exploring microbial diversity and biosynthetic potential in zoo and wildlife animal microbiomes.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {8263},
pmid = {39327429},
issn = {2041-1723},
support = {469073465//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {Animals ; *Animals, Wild/microbiology ; *Animals, Zoo/microbiology ; *Gastrointestinal Microbiome/genetics ; *Anti-Bacterial Agents/pharmacology ; *Microbiota/genetics/drug effects ; Bacteria/genetics/metabolism/classification/drug effects ; Multigene Family ; Humans ; Biodiversity ; Drug Resistance, Bacterial/genetics ; Vancomycin/pharmacology ; Biosynthetic Pathways/genetics ; },
abstract = {Understanding human, animal, and environmental microbiota is essential for advancing global health and combating antimicrobial resistance (AMR). We investigate the oral and gut microbiota of 48 animal species in captivity, comparing them to those of wildlife animals. Specifically, we characterize the microbiota composition, metabolic pathways, AMR genes, and biosynthetic gene clusters (BGCs) encoding the production of specialized metabolites. Our results reveal a high diversity of microbiota, with 585 novel species-level genome bins (SGBs) and 484 complete BGCs identified. Functional gene analysis of microbiomes shows diet-dependent variations. Furthermore, by comparing our findings to wildlife-derived microbiomes, we observe the impact of captivity on the animal microbiome, including examples of converging microbiome compositions. Importantly, our study identifies AMR genes against commonly used veterinary antibiotics, as well as resistance to vancomycin, a critical antibiotic in human medicine. These findings underscore the importance of the 'One Health' approach and the potential for zoonotic transmission of pathogenic bacteria and AMR. Overall, our study contributes to a better understanding of the complexity of the animal microbiome and highlights its BGC diversity relevant to the discovery of novel antimicrobial compounds.},
}
@article {pmid39331712,
year = {2024},
author = {Fellows, RC and Chun, SK and Larson, N and Fortin, BM and Mahieu, AL and Song, WA and Seldin, MM and Pannunzio, NR and Masri, S},
title = {Disruption of the intestinal clock drives dysbiosis and impaired barrier function in colorectal cancer.},
journal = {Science advances},
volume = {10},
number = {39},
pages = {eado1458},
doi = {10.1126/sciadv.ado1458},
pmid = {39331712},
issn = {2375-2548},
mesh = {Animals ; *Colorectal Neoplasms/microbiology/metabolism/pathology ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology ; Mice ; *Circadian Clocks/genetics ; Intestinal Mucosa/metabolism/microbiology ; Disease Models, Animal ; Humans ; Permeability ; },
abstract = {Diet is a robust entrainment cue that regulates diurnal rhythms of the gut microbiome. We and others have shown that disruption of the circadian clock drives the progression of colorectal cancer (CRC). While certain bacterial species have been suggested to play driver roles in CRC, it is unknown whether the intestinal clock impinges on the microbiome to accelerate CRC pathogenesis. To address this, genetic disruption of the circadian clock, in an Apc-driven mouse model of CRC, was used to define the impact on the gut microbiome. When clock disruption is combined with CRC, metagenomic sequencing identified dysregulation of many bacterial genera including Bacteroides, Helicobacter, and Megasphaera. We identify functional changes to microbial pathways including dysregulated nucleic acid, amino acid, and carbohydrate metabolism, as well as disruption of intestinal barrier function. Our findings suggest that clock disruption impinges on microbiota composition and intestinal permeability that may contribute to CRC pathogenesis.},
}
@article {pmid39331699,
year = {2024},
author = {Yang, Z and Shan, Y and Liu, X and Chen, G and Pan, Y and Gou, Q and Zou, J and Chang, Z and Zeng, Q and Yang, C and Kong, J and Sun, Y and Li, S and Zhang, X and Wu, WC and Li, C and Peng, H and Holmes, EC and Guo, D and Shi, M},
title = {VirID: Beyond Virus Discovery - An Integrated Platform for Comprehensive RNA Virus Characterization.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msae202},
pmid = {39331699},
issn = {1537-1719},
abstract = {RNA viruses exhibit vast phylogenetic diversity and can significantly impact public health and agriculture. However, current bioinformatics tools for viral discovery from metagenomic data frequently generate false positive virus results, overestimate viral diversity, and misclassify virus sequences. Additionally, current tools often fail to determine virus-host associations, which hampers investigation of the potential threat posed by a newly detected virus. To address these issues we developed VirID, a software tool specifically designed for the discovery and characterization of RNA viruses from metagenomic data. The basis of VirID is a comprehensive RNA-dependent RNA polymerase (RdRP) database to enhance a workflow that includes RNA virus discovery, phylogenetic analysis, and phylogeny-based virus characterization. Benchmark tests on a simulated data set demonstrated that VirID had high accuracy in profiling viruses and estimating viral richness. In evaluations with real-world samples, VirID was able to identity RNA viruses of all type, but also provided accurate estimations of viral genetic diversity and virus classification, as well as comprehensive insights into virus associations with humans, animals, and plants. VirID therefore offers a robust tool for virus discovery and serves as a valuable resource in basic virological studies, pathogen surveillance, and early warning systems for infectious disease outbreaks.},
}
@article {pmid39331310,
year = {2024},
author = {Deézsi-Magyar, N and Novák, N and Lukács, A and Tarcsai, KR and Hajdu, &#xc1; and Takács, L and Farkas, FB and Rigó, Z and Barcsay, E and Kis, Z and Szomor, K},
title = {First whole genome sequencing and analysis of human parechovirus type 3 causing a healthcare-associated outbreak among neonates in Hungary.},
journal = {European journal of clinical microbiology &amp; infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {},
number = {},
pages = {},
pmid = {39331310},
issn = {1435-4373},
abstract = {PURPOSE: In November 2023, the National Reference Laboratory for Enteroviruses (Budapest, Hungary) received stool, pharyngeal swab and cerebrospinal fluid samples from five newborns suspected of having human parechovirus (PEV-A) infection. The neonates were born in the same hospital and presented with fever and sepsis-like symptoms at 8-9 days of age, and three of them showed symptoms consistent with central nervous system involvement. PEV-A positivity was confirmed by quantitative reverse transcription polymerase chain reaction.<br><br>METHODS: To determine the PEV-A genotype responsible for the infections, fecal samples of four neonates were subjected to metagenomic sequencing. For further analyses, amplicon-based whole genome sequencing was performed directly from the clinical samples.<br><br>RESULTS: On the basis of whole genome analysis, sequences were allocated to PEV-A genotype 3 (PEV-A3) and consensus sequences were identical. Two ambiguities were identified in the viral protein 1 (VP1) region of all sequences at a frequency of 17.7-53.7%, indicating the simultaneous presence of at least two quasispecies in the clinical samples. The phylogenetic analysis and similarity plotting showed that all sequences clustered without any topological inconsistencies between the P1 capsid and P2, P3 non-capsid regions, suggesting that recombination events during evolution were unlikely.<br><br>CONCLUSION: Our findings suggest that the apparent cluster of cases were microbiologically related, and the results may also inform future investigations on the evolution and pathogenicity of PEV-A3 infections.},
}
@article {pmid39330355,
year = {2024},
author = {Abbà, S and Valentini, B and Stefanini, I},
title = {Fungal Identifier (FId): An Updated Polymerase Chain Reaction-Restriction Fragment Length Polymorphism Approach to Ease Ascomycetous Yeast Isolates' Identification in Ecological Studies.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {10},
number = {9},
pages = {},
doi = {10.3390/jof10090595},
pmid = {39330355},
issn = {2309-608X},
support = {RGP0060/2021//HFSP/ ; 20225SXSHY//PRIN 2022/ ; },
abstract = {Culturomics has been temporarily exceeded by the advent of omics approaches such as metabarcoding and metagenomics. However, despite improving our knowledge of microbial population composition, both metabarcoding and metagenomics are not suitable for investigating and experimental testing inferences about microbial ecological roles and evolution. This leads to a recent revival of culturomics approaches, which should be supported by improvements in the available tools for high-throughput microbial identification. This study aimed to update the classical PCR-RFLP approach in light of the currently available knowledge on yeast genomics. We generated and analyzed a database including more than 1400 ascomycetous yeast species, each characterized by PCR-RFLP profiles obtained with 143 different endonucleases. The results allowed for the in silico evaluation of the performance of the tested endonucleases in the yeast species' identification and the generation of FId (Fungal Identifier), an online freely accessible tool for the identification of yeast species according to experimentally obtained PCR-RFLP profiles.},
}
@article {pmid39329490,
year = {2024},
author = {Maday, SDM and Kingsbury, JM and Weaver, L and Pantos, O and Wallbank, JA and Doake, F and Masterton, H and Hopkins, M and Dunlop, R and Gaw, S and Theobald, B and Risani, R and Abbel, R and Smith, D and Handley, KM and Lear, G},
title = {Taxonomic variation, plastic degradation, and antibiotic resistance traits of plastisphere communities in the maturation pond of a wastewater treatment plant.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0071524},
doi = {10.1128/aem.00715-24},
pmid = {39329490},
issn = {1098-5336},
abstract = {Wastewater treatment facilities can filter out some plastics before they reach the open environment, yet microplastics often persist throughout these systems. As they age, microplastics in wastewater may both leach and sorb pollutants and fragment to provide an increased surface area for bacterial attachment and conjugation, possibly impacting antimicrobial resistance (AMR) traits. Despite this, little is known about the effects of persistent plastic pollution on microbial functioning. To address this knowledge gap, we deployed five different artificially weathered plastic types and a glass control into the final maturation pond of a municipal wastewater treatment plant in Ōtautahi-Christchurch, Aotearoa/New Zealand. We sampled the plastic-associated biofilms (plastisphere) at 2, 6, 26, and 52 weeks, along with the ambient pond water, at three different depths (20, 40, and 60 cm from the pond water surface). We investigated the changes in plastisphere microbial diversity and functional potential through metagenomic sequencing. Bacterial 16S ribosomal RNA genes composition did not vary among plastic types and glass controls (P = 0.997) but varied among sampling times [permutational multivariate analysis of variance (PERMANOVA), P = 0.001] and depths (PERMANOVA, P = 0.011). Overall, there was no polymer-substrate specificity evident in the total composition of genes (PERMANOVA, P = 0.67), but sampling time (PERMANOVA, P = 0.002) and depth were significant factors (PERMANOVA, P = 0.001). The plastisphere housed diverse AMR gene families, potentially influenced by biofilm-meditated conjugation. The plastisphere also harbored an increased abundance of genes associated with the biodegradation of nylon, or nylon-associated substances, including nylon oligomer-degrading enzymes and hydrolases.IMPORTANCEPlastic pollution is pervasive and ubiquitous. Occurrences of plastics causing entanglement or ingestion, the leaching of toxic additives and persistent organic pollutants from environmental plastics, and their consequences for marine macrofauna are widely reported. However, little is known about the effects of persistent plastic pollution on microbial functioning. Shotgun metagenomics sequencing provides us with the necessary tools to examine broad-scale community functioning to further investigate how plastics influence microbial communities. This study provides insight into the functional consequence of continued exposure to waste plastic by comparing the prokaryotic functional potential of biofilms on five types of plastic [linear low-density polyethylene (LLDPE), nylon-6, polyethylene terephthalate, polylactic acid, and oxygen-degradable LLDPE], glass, and ambient pond water over 12 months and at different depths (20, 40, and 60 cm) within a tertiary maturation pond of a municipal wastewater treatment plant.},
}
@article {pmid39329142,
year = {2024},
author = {Khomutovska, N and Jasser, I and Sarapultseva, P and Spirina, V and Zaitsev, A and Masłowiecka, J and Isidorov, VA},
title = {Seasonal dynamics in leaf litter decomposing microbial communities in temperate forests: a whole-genome- sequencing-based study.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e17769},
pmid = {39329142},
issn = {2167-8359},
mesh = {*Plant Leaves/microbiology/metabolism ; *Forests ; *Seasons ; *Microbiota/genetics/physiology ; Bacteria/genetics/classification/metabolism ; Fungi/genetics/classification/metabolism/isolation &amp; purification ; Whole Genome Sequencing ; Metagenome/genetics ; Trees/microbiology ; },
abstract = {Leaf litter decomposition, a crucial component of the global carbon cycle, relies on the pivotal role played by microorganisms. However, despite their ecological importance, leaf-litter-decomposing microorganism taxonomic and functional diversity needs additional study. This study explores the taxonomic composition, dynamics, and functional role of microbial communities that decompose leaf litter of forest-forming tree species in two ecologically unique regions of Europe. Twenty-nine microbial metagenomes isolated from the leaf litter of eight forest-forming species of woody plants were investigated by Illumina technology using read- and assembly-based approaches of sequences analysis. The taxonomic structure of the microbial community varies depending on the stage of litter decomposition; however, the community's core is formed by Pseudomonas, Sphingomonas, Stenotrophomonas, and Pedobacter genera of Bacteria and by Aureobasidium, Penicillium, Venturia genera of Fungi. A comparative analysis of the taxonomic structure and composition of the microbial communities revealed that in both regions, seasonal changes in structure take place; however, there is no clear pattern in its dynamics. Functional gene analysis of MAGs revealed numerous metabolic profiles associated with leaf litter degradation. This highlights the diverse metabolic capabilities of microbial communities and their implications for ecosystem processes, including the production of volatile organic compounds (VOCs) during organic matter decomposition. This study provides important advances in understanding of ecosystem processes and the carbon cycle, underscoring the need to unravel the intricacies of microbial communities within these contexts.},
}
@article {pmid39328911,
year = {2024},
author = {Lemos Junior, WJF and Marques Costa, L and Alberto Guerra, C and Sales de Oliveira, V and Gava Barreto, A and Alves de Oliveira, F and de Paula, BP and Esmerino, EA and Corich, V and Giacomini, A and Guerra, AF},
title = {Microbial landscape of cooked meat products: evaluating quality and safety in vacuum-packaged sausages using culture-dependent and culture-independent methods over 1 year in a sustainable food chain.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1457819},
pmid = {39328911},
issn = {1664-302X},
abstract = {Over the last few decades, advancements in process safety and quality methods have been significantly improved, yet new challenges continue to emerge in the sustainable food supply chain. This study aimed to investigate some physicochemical and microbiological parameters impacting meat products, particularly cooked sausages, within a sustainable supply chain, focusing on quality, spoilage populations, and syneresis formation under vacuum conditions. A comprehensive analysis was conducted on 355 samples collected over four seasons using high-throughput sequencing (16S/ITS) and microbiological and physicochemical [pH and water activity (aw)] assessments. The microbial growth predictor MicroLab_ShelfLife was employed, and multiple factor analysis (MFA) and agglomerative hierarchical clustering (AHC) were utilized to understand how these variables influence the microbiome resilience of these products. Lactic and acetic acids were correlated with the microbiome of the sausages and the liquid coating covering them using metagenomic analyses. The study highlighted that 52% of the evaluated meat industries in southeastern Brazil are implementing effective protocols for sustainable chain production. The results indicated that the durability of vacuum-packaged cooked sausages was primarily influenced by storage temperature (RV coefficient of 0.906), initial microbial load (0.755), and aw (0.624). Average microbial counts were 4.30 log cfu/g (initial), 4.61 (7°C/4 days), 4.90 (7°C/8 days), 6.06 (36°C/4 days), and 6.79 (36°C/8 days). Seasonal durability analysis revealed that winter had the highest average durability of 45.58 days, while summer had the lowest at 26.33 days. Yeast populations, including Trichosporon sp. and Candida sp., were identified as key genera influencing spoilage dynamics. In addition, Bacillus species emerged as dominant spoilage microorganisms, highlighting the need for new critical controls. This study demonstrates the impact of metagenomic approaches, including ITS and 16S amplicon sequencing, in revealing microbial community dynamics, storage temperature, and aw, which are essential for developing targeted interventions to enhance food safety and quality sustainably.},
}
@article {pmid39328895,
year = {2024},
author = {McAdams, ZL and Yates, J and Turner, G and Dorfmeyer, RA and Wight-Carter, M and Amos-Landgraf, J and Franklin, CL and Ericsson, AC},
title = {Effect of shipping on the microbiome of donor mice used to reconstitute germ-free recipients.},
journal = {Gut microbes reports},
volume = {1},
number = {1},
pages = {1-8},
pmid = {39328895},
issn = {2993-3935},
abstract = {The gut microbiota (GM) influences multiple processes during host development and maintenance. To study these events, fecal microbiota transfer (FMT) to germ-free (GF) recipients is often performed. Mouse models of disease are also susceptible to GM-dependent effects, and cryo-repositories often store feces from donated mouse strains. Shipping live mice may affect the GM and result in an inaccurate representation of the baseline GM. We hypothesize that the use of such fecal samples for FMT would transfer shipping-induced changes in the donor GM to GF recipients. To test this, donor mice originating from two suppliers were shipped to the University of Missouri. Fecal samples collected pre- and post-shipping were used to inoculate GF mice. Pre- and post-shipping fecal samples from donors, and fecal and/or cecal contents were collected from recipients at one and two weeks post-FMT. 16S rRNA sequencing revealed supplier-dependent effects of shipping on the donor microbiome. FMT efficiency was independent of shipping timepoint or supplier, resulting in transmission of shipping-induced changes to recipient mice, however the effect of supplier-origin microbiome remained evident. While shipping may cause subtle changes in fecal samples collected for FMT, such effects are inconsistent among supplier-origin GMs and minor in comparison to other biological variables.},
}
@article {pmid39328586,
year = {2024},
author = {Huang, M and Jiang, N and Ren, Y and Peng, Y and Wu, X},
title = {Very severe aplastic anemia in a child with pulmonary mucormycosis: a case report.},
journal = {Frontiers in pediatrics},
volume = {12},
number = {},
pages = {1453059},
pmid = {39328586},
issn = {2296-2360},
abstract = {Aplastic anemia (AA), is a rare but potentially life-threatening disease characterized by pancytopenia and a hypocellular bone marrow. Pulmonary mucormycosis (PM) is a rare but life-threatening fungal infection observed in immunocompromised patients, particularly those with neutropenia and those using corticosteroids, with a high mortality rate from 40 to 80%. However, PM diagnosis and treatment remain challenging. This study reports a case of very severe aplastic anemia (VSAA) in a male child with PM. The innovation of this article lies in the following aspects: the patient exhibited typical clinical manifestations, the reverse halo sign (RHS) on chest computed tomography (CT), and a positive metagenomic next-generation sequencing (mNGS) analysis; despite aggressive anti-infective treatment and left lower lobectomy, he experienced a poor clinical outcome. Reflecting on cases with poor prognosis can indeed offer valuable insights and opportunities for learning. This study underlines the diagnostic challenges in mucormycosis, which should be considered in persistent fever that is unresponsive to standard antibiotic and antifungal therapies, and conduct a comprehensive examination to achieve early detection, diagnosis and treatment. It was concluded that, in addition to antifungal treatment, early surgery is essential for treating mucormycosis.},
}
@article {pmid39328446,
year = {2024},
author = {Sizova, EA and Yausheva, EV and Nechitailo, KS and Kamirova, AM and Ryazanceva, KV and Shoshin, DE and Skalny, AV and Tinkov, AA},
title = {Influence of the Saccharomyces cerevisiae-based probiotic complex on gut microbiota, serum biochemistry, and circulating trace element and mineral levels in lactating dairy cows.},
journal = {Veterinary world},
volume = {17},
number = {8},
pages = {1864-1871},
pmid = {39328446},
issn = {0972-8988},
abstract = {BACKGROUND AND AIM: The existing data demonstrate that gut microbiota is involved in regulating mineral metabolism in cattle, although the data are quite contradictory. The study aimed to evaluate Saccharomyces cerevisiae-based probiotic's effects on gut microbiota, systemic metabolism, and dairy cows' essential trace element and mineral body burden.<br><br>MATERIALS AND METHODS: Fifteen cows received a daily supplement of a 50 g S. cerevisiae-based probiotic, fortified with methionine, choline, eugenol, cinnamaldehyde, and Capsicum oleoresin, for a month. 16S metagenomic sequencing was used to evaluate the taxonomic features of fecal microbiota. Serum trace elements and minerals levels were determined through inductively coupled plasma mass spectrometry.<br><br>RESULTS: Supplementation with S. cerevisiae-based probiotic complex significantly increased alpha and beta diversity, as well as the abundance of Mediterranea and Clostridium IV within the Bacillota phylum, whereas that of Bacteroidota and specifically unclassified Bacteroidales and unclassified Oscillospiraceae decreased. Following probiotic supplementation with the S. cerevisiae-based complex, gut microbiota modulation led to a significant boost in circulating levels of calcium, copper, selenium, and zinc. Creatinine levels decreased while total cholesterol levels increased within normal limits in the serum analysis.<br><br>CONCLUSION: The observed improvement in trace elements and minerals in dairy cows might be due to changes in intestinal microflora caused by supplementation. Therefore, probiotic supplementation in cattle may be considered a potential tool for improvement of mineral nutrition in cattle. However, the influence of probiotic treatment and modulation of mineral metabolism on milk productivity and overall performance in cattle is yet to be estimated.},
}
@article {pmid39328398,
year = {2024},
author = {Abuljadayel, D and Alotibi, A and Algothmi, K and Basingab, F and Alhazmi, S and Almuhammadi, A and Alharthi, A and Alyoubi, R and Bahieldin, A},
title = {Gut microbiota of children with autism spectrum disorder and healthy siblings: A comparative study.},
journal = {Experimental and therapeutic medicine},
volume = {28},
number = {5},
pages = {430},
pmid = {39328398},
issn = {1792-1015},
abstract = {Autism spectrum disorder (ASD) is a neurodevelopmental abnormality that impairs social communication. The human gut microbiome (GM) influences a variety of local processes, including dysbiosis and the defense against pathogenic microorganisms. The aim of the present study was to categorize and identify molecular biomarkers for ASD. In the present study, metagenomics whole genome shotgun sequencing was used to identify the gut microbiota in autistic individuals. Fecal samples from four children with ASD and four healthy control siblings, aged 3-10 years old, were examined using bioinformatics analysis. A total of 673,091 genes were cataloged, encompassing 25 phyla and 2 kingdoms based on the taxonomy analysis. The results revealed 257 families, 34 classes, 84 orders, and 1,314 genera among 4,339 species. The top 10 most abundant genes and corresponding functional genes for each group were determined after the abundance profile was screened. The results showed that children with ASD had a higher abundance of certain gut microbiomes than their normal siblings and vice versa. The phyla Firmicutes and Proteobacteria were the most abundant in ASD. The Thermoanaerobacteria class was also restricted to younger healthy individuals. Moreover, the Lactobacillaceae family was more abundant in children with ASD. Additionally, it was discovered that children with ASD had a higher abundance of the Bacteroides genus and a lower abundance of the Bifidobacterium and Prevotella genera. In conclusion, there were more pathogenic genera and species and higher levels of biomass, diversity and richness in the GM of children with ASD.},
}
@article {pmid39328319,
year = {2024},
author = {Chen, Y and Lan, P and Liu, L and Zhou, K},
title = {Prone positioning ventilation treatment rescuing a patient with chlamydia abortus-induced ARDS diagnosed by next generation sequencing: a case report.},
journal = {Frontiers in medicine},
volume = {11},
number = {},
pages = {1428300},
pmid = {39328319},
issn = {2296-858X},
abstract = {BACKGROUND: Chlamydia abortus is a pathogen capable of infecting both humans and animals. In most known cases, this pathogen primarily infects pregnant women, leading to miscarriage and preterm birth. However, it is exceedingly rare for this pathogen to cause pneumonia that progresses to severe Acute Respiratory Distress Syndrome (ARDS).<br><br>CASE INTRODUCTION: We present a case of a 76-year-old male patient who was clinically diagnosed with Acute Respiratory Distress Syndrome (ARDS) caused by Chlamydia abortus and successfully treated. The patient's condition rapidly deteriorated over six days, evolving from a lung infection to severe pneumonia, ultimately leading to ARDS and sepsis. Initially, he was admitted to a local hospital for a lung infection where routine etiological examinations failed to identify any significant pathogens, and he received only empirical antimicrobial therapy. However, the lung infection was not controlled, and the patient's condition rapidly worsened, resulting in severe respiratory distress. This necessitated tracheal intubation and assisted ventilation, after which he was transferred to our hospital for treatment. Due to the patient's family's inability to afford the cost of ECMO treatment, we adopted a prone positioning ventilation strategy to improve the patient's ventilation-perfusion matching. Additionally, we performed metagenomic next-generation sequencing on the patient's bronchoalveolar lavage fluid, which confirmed the infection with Chlamydia abortus. These measures ultimately led to the successful treatment of the patient.<br><br>CONCLUSION: Chlamydia abortus infection can lead to severe ARDS, necessitating timely diagnosis and active intervention by clinicians. This case highlights the crucial role of metagenomic next-generation sequencing in diagnosing rare pathogens. Timely adoption of prone positioning ventilation can significantly improve ventilation-perfusion matching, effectively treating ARDS caused by Chlamydia abortus. Additionally, the combination of moxifloxacin and piperacillin-tazobactam can treat ARDS caused by Chlamydia abortus.},
}
@article {pmid39327897,
year = {2024},
author = {Dai, Z and Wang, H and Xu, J and Lu, X and Ni, P and Yang, S and Shen, Q and Wang, X and Li, W and Wang, X and Zhou, C and Zhang, W and Shan, T},
title = {Unveiling the Virome of Wild Birds: Exploring CRESS-DNA Viral Dark Matter.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evae206},
pmid = {39327897},
issn = {1759-6653},
abstract = {Amid global health concerns and the constant threat of zoonotic diseases, this study delves into the diversity of circular replicase-encoding single-stranded DNA (CRESS-DNA) viruses within Chinese wild bird populations. Employing viral metagenomics to tackle the challenge of "viral dark matter, " the research collected and analyzed 3,404 cloacal swab specimens across 26 bird families. Metagenomic analysis uncovered a rich viral landscape, with 67.48% of reads classified as viral dark matter, spanning multiple taxonomic levels. Notably, certain viral families exhibited host-specific abundance patterns, with Galliformes displaying the highest diversity. Diversity analysis categorized samples into distinct groups, revealing significant differences in viral community structure, particularly noting higher diversity in terrestrial birds compared to songbirds and unique diversity in migratory birds versus perching birds. The identification of ten novel Circoviridae viruses, seven Smacoviridae viruses, and 167 Genomoviridae viruses, along with 100 unclassified CRESS-DNA viruses, underscores the expansion of knowledge on avian-associated circular DNA viruses. Phylogenetic and structural analyses of Rep proteins offered insights into evolutionary relationships and potential functional variations among CRESS-DNA viruses. In conclusion, this study significantly enhances our understanding of the avian virome, shedding light on the intricate relationships between viral communities and host characteristics in Chinese wild bird populations. The diverse array of CRESS-DNA viruses discovered opens avenues for future research into viral evolution, spread factors, and potential ecosystem impacts.},
}
@article {pmid39327796,
year = {2024},
author = {McLeish, M and Peláez, A and Pagán, I and Gavilán, RG and Fraile, A and García-Arenal, F},
title = {Plant virus community structuring is shaped by habitat heterogeneity and traits for host plant resource utilisation.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.20054},
pmid = {39327796},
issn = {1469-8137},
support = {BES-2016-077810//Formaci&#xf3;n de Personal Investigador/ ; PID2021-124671OB-I00//Agencia Nacional de Investigaci&#xf3;n e Innovaci&#xf3;n/ ; RTI2018-094302-B-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; },
abstract = {Host plants provide resources critical to viruses and the spatial structuring of plant communities affects the niches available for colonisation and disease emergence. However, large gaps remain in the understanding of mechanisms that govern plant-virus disease ecology across heterogeneous plant assemblages. We combine high-throughput sequencing, network, and metacommunity approaches to test whether habitat heterogeneity in plant community composition corresponded with virus resource utilisation traits of transmission mode and host range. A majority of viruses exhibited habitat specificity, with communities connected by key generalist viruses and potential host reservoirs. There was an association between habitat heterogeneity and virus community structuring, and between virus community structuring and resource utilisation traits of host range and transmission. The relationship between virus species distributions and virus trait responses to habitat heterogeneity was scale-dependent, being stronger at finer (site) than larger (habitat) spatial scales. Results indicate that habitat heterogeneity has a part in plant virus community assembly, and virus community structuring corresponds to virus trait responses that vary with the scale of observation. Distinctions in virus communities caused by plant resource compartmentalisation can be used to track trait responses of viruses to hosts important in forecasting disease emergence.},
}
@article {pmid39327508,
year = {2024},
author = {Akhtar, A and Lata, M and Sunsunwal, S and Yadav, A and Lnu, K and Subramanian, S and Ramya, TNC},
title = {Author Correction: New carbohydrate binding domains identified by phage display based functional metagenomic screens of human gut microbiota.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {1190},
doi = {10.1038/s42003-024-06920-0},
pmid = {39327508},
issn = {2399-3642},
}
@article {pmid39327484,
year = {2024},
author = {Kazantseva, E and Donmez, A and Frolova, M and Pop, M and Kolmogorov, M},
title = {Strainy: phasing and assembly of strain haplotypes from long-read metagenome sequencing.},
journal = {Nature methods},
volume = {},
number = {},
pages = {},
pmid = {39327484},
issn = {1548-7105},
support = {Intramural Research Program of the Center for Cancer Research//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; Intramural Research Program of the Center for Cancer Research//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; },
abstract = {Bacterial species in microbial communities are often represented by mixtures of strains, distinguished by small variations in their genomes. Short-read approaches can be used to detect small-scale variation between strains but fail to phase these variants into contiguous haplotypes. Long-read metagenome assemblers can generate contiguous bacterial chromosomes but often suppress strain-level variation in favor of species-level consensus. Here we present Strainy, an algorithm for strain-level metagenome assembly and phasing from Nanopore and PacBio reads. Strainy takes a de novo metagenomic assembly as input and identifies strain variants, which are then phased and assembled into contiguous haplotypes. Using simulated and mock Nanopore and PacBio metagenome data, we show that Strainy assembles accurate and complete strain haplotypes, outperforming current Nanopore-based methods and comparable with PacBio-based algorithms in completeness and accuracy. We then use Strainy to assemble strain haplotypes of a complex environmental metagenome, revealing distinct strain distribution and mutational patterns in bacterial species.},
}
@article {pmid39327438,
year = {2024},
author = {Schmartz, GP and Rehner, J and Gund, MP and Keller, V and Molano, LG and Rupf, S and Hannig, M and Berger, T and Flockerzi, E and Seitz, B and Fleser, S and Schmitt-Grohé, S and Kalefack, S and Zemlin, M and Kunz, M and Götzinger, F and Gevaerd, C and Vogt, T and Reichrath, J and Diehl, L and Hecksteden, A and Meyer, T and Herr, C and Gurevich, A and Krug, D and Hegemann, J and Bozhueyuek, K and Gulder, TAM and Fu, C and Beemelmanns, C and Schattenberg, JM and Kalinina, OV and Becker, A and Unger, M and Ludwig, N and Seibert, M and Stein, ML and Hanna, NL and Martin, MC and Mahfoud, F and Krawczyk, M and Becker, SL and Müller, R and Bals, R and Keller, A},
title = {Decoding the diagnostic and therapeutic potential of microbiota using pan-body pan-disease microbiomics.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {8261},
pmid = {39327438},
issn = {2041-1723},
mesh = {Humans ; *Microbiota/genetics ; *Metagenome/genetics ; *Metagenomics/methods ; Bacteria/genetics/isolation &amp; purification/classification ; Feces/microbiology ; Male ; Female ; Multigene Family ; Saliva/microbiology ; Adult ; },
abstract = {The human microbiome emerges as a promising reservoir for diagnostic markers and therapeutics. Since host-associated microbiomes at various body sites differ and diseases do not occur in isolation, a comprehensive analysis strategy highlighting the full potential of microbiomes should include diverse specimen types and various diseases. To ensure robust data quality and comparability across specimen types and diseases, we employ standardized protocols to generate sequencing data from 1931 prospectively collected specimens, including from saliva, plaque, skin, throat, eye, and stool, with an average sequencing depth of 5.3 gigabases. Collected from 515 patients, these samples yield an average of 3.7 metagenomes per patient. Our results suggest significant microbial variations across diseases and specimen types, including unexpected anatomical sites. We identify 583 unexplored species-level genome bins (SGBs) of which 189 are significantly disease-associated. Of note, the existence of microbial resistance genes in one specimen was indicative of the same resistance genes in other specimens of the same patient. Annotated and previously undescribed SGBs collectively harbor 28,315 potential biosynthetic gene clusters (BGCs), with 1050 significant correlations to diseases. Our combinatorial approach identifies distinct SGBs and BGCs, emphasizing the value of pan-body pan-disease microbiomics as a source for diagnostic and therapeutic strategies.},
}
@article {pmid39327011,
year = {2024},
author = {Ruff, SE and Schwab, L and Vidal, E and Hemingway, J and Kraft, B and Murali, R},
title = {Widespread occurrence of dissolved oxygen anomalies, aerobic microbes, and oxygen-producing metabolic pathways in apparently anoxic environments.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiae132},
pmid = {39327011},
issn = {1574-6941},
abstract = {Nearly all molecular oxygen (O2) on Earth is produced via oxygenic photosynthesis by plants or photosynthetically active microorganisms. Light-independent O2 production, which occurs both abiotically, e.g., through water radiolysis, or biotically, e.g., through the dismutation of nitric oxide or chlorite, has been thought to be negligible to the Earth system. However, recent work indicates that O2 is produced and consumed in dark and apparently anoxic environments at a much larger scale than assumed. Studies have shown that isotopically light O2 can accumulate in old groundwaters; that strictly aerobic microorganisms are present in many apparently anoxic habitats; and that microbes and metabolisms that can produce O2 without light are widespread and abundant in diverse ecosystems. Analysis of published metagenomic data reveals that the enzyme putatively capable of nitric oxide dismutation (NOD) forms four major phylogenetic clusters and occurs in at least 16 bacterial phyla most notably the Bacteroidota. Similarly, a re-analysis of published isotopic signatures of dissolved O2 in groundwater suggests in-situ production in up to half of the studied ecosystems. Geochemical and microbiological data supports the conclusion that "dark oxygen" production is an important and widespread yet overlooked process in apparently anoxic environments with far-reaching implications for subsurface biogeochemistry and ecology.},
}
@article {pmid39326916,
year = {2024},
author = {Zhu, Z and Shibata, R and Hoffman, KL and Cormier, J and Mansbach, JM and Liang, L and Camargo, CA and Hasegawa, K},
title = {Integrated nasopharyngeal airway metagenome and asthma genetic risk endotyping of severe bronchiolitis in infancy and risk of childhood asthma.},
journal = {The European respiratory journal},
volume = {},
number = {},
pages = {},
doi = {10.1183/13993003.01130-2024},
pmid = {39326916},
issn = {1399-3003},
abstract = {UNLABELLED: The severe bronchiolitis endotype characterized by a high abundance of H. influenzae, high proportion of RV-A and RV-C infections, and high asthma genetic risk had a significantly higher risk for developing asthma.<br><br>BACKGROUND: Infants with bronchiolitis are at increased risk for developing asthma. Growing evidence suggests bronchiolitis is a heterogeneous condition. However, little is known about its biologically distinct subgroups based on the integrated metagenome and asthma genetic risk signature and their longitudinal relationships with asthma development.<br><br>METHODS: In a multi-center prospective cohort study of infants with severe bronchiolitis (i.e., bronchiolitis requiring hospitalization), we profiled nasopharyngeal airway metagenome and virus at hospitalization, and calculated the polygenic risk score of asthma. Using similarity network fusion clustering approach, we identified integrated metagenome-asthma genetic risk endotypes. We also examined their longitudinal association with the risk of developing asthma by age six years.<br><br>RESULTS: Of 450 infants with bronchiolitis (median age, 3&#x2005;months), we identified five distinct endotypes-characterized by their nasopharyngeal metagenome, virus, and asthma genetic risk profiles. Compared with endotype A infants (who clinically resembled "classic" bronchiolitis), endotype E infants (characterized by a high abundance of H. influenzae, high proportion of RV-A and RV-C infections, and high asthma genetic risk) had a significantly higher risk for developing asthma (35.9% versus 16.7%; ORadj, 2.24; 95%CI, 1.02-4.97; p=0.046). The pathway analysis showed that endotype E had enriched microbial pathways (e.g., glycolysis, L-lysine, arginine metabolism) and host pathways (e.g., IFNs, IL-6/JAK/STAT3, fatty acids, MHC, and immunoglobin-related) (FDR<0.05). Additionally, endotype E had a significantly higher proportion of neutrophils (FDR<0.05).<br><br>CONCLUSION: In this multi-center prospective cohort study of infant bronchiolitis, the clustering analysis of integrated-omics data identified biologically distinct endotypes with differential risks for developing asthma.},
}
@article {pmid39326354,
year = {2024},
author = {Li, J and Li, X and Zuo, R and Yang, L and Xu, Y and Yu, S and Wang, J and Yang, J},
title = {Exploring the microbe-mediated biological processes of BTEX and toxic metal(loid)s in aging petrochemical landfills.},
journal = {Ecotoxicology and environmental safety},
volume = {285},
number = {},
pages = {117103},
doi = {10.1016/j.ecoenv.2024.117103},
pmid = {39326354},
issn = {1090-2414},
abstract = {Aging petrochemical landfills serve as reservoirs of inorganic and organic contaminants, posing potential risks of contamination to the surrounding environment. Identifying the pollution characteristics and elucidating the translocation/ transformation processes of typical contaminants in aging petrochemical landfills are crucial yet challenging endeavors. In this study, we employed a combination of chemical analysis and microbial metagenomic technologies to investigate the pollution characteristics of benzene, toluene, ethylbenzene, and xylene (BTEX) as well as metal(loid)s in a representative aging landfill, surrounding soils, and underlying groundwater. Furthermore, we aimed to explore their transformations driven by microbial activity. Our findings revealed widespread distribution of metal(loid)s, including Cd, Ni, Cu, As, Mn, Pb, and Zn, in these environmental media, surpassing soil background values and posing potential ecological risks. Additionally, microbial processes were observed to contribute significantly to the degradation of BTEX compounds and the transformation of metal(loid)s in landfills and surrounding soils, with identified microbial communities and functions playing key roles. Notably, co-occurrence network analysis unveiled the coexistence of functional genes associated with BTEX degradation and metal(loid) transformation, driven primarily by As, Ni, and Cd. These results shed light on the co-selection of resistance traits against BTEX and metal(loid) contaminants in soil microbial consortia under co-contamination scenarios, supporting microbial adaptive evolution in aging petrochemical landfills. The insights gained from this study enhance our understanding of characteristic pollutants and microbial transformation processes in aging landfills, thereby facilitating improved landfill management and contamination remediation strategies.},
}
@article {pmid39326312,
year = {2024},
author = {Wang, X and Cui, J and Gu, Z and Guo, L and Liu, R and Guo, Y and Qin, N and Yang, Y},
title = {Aged garlic oligosaccharides modulate host metabolism and gut microbiota to alleviate high-fat and high-cholesterol diet-induced atherosclerosis in ApoE[-/-] mice.},
journal = {Food chemistry},
volume = {463},
number = {Pt 3},
pages = {141409},
doi = {10.1016/j.foodchem.2024.141409},
pmid = {39326312},
issn = {1873-7072},
abstract = {Atherosclerosis (AS) is a cardiovascular disease caused by excessive accumulation of lipids in arterial walls. In this study, we developed an AS model in ApoE[-/-] mice using a high-fat, high-cholesterol diet and investigated the anti-AS mechanism of aged garlic oligosaccharides (AGOs) by focusing on the gut microbiota. Results revealed that AGOs exhibited significant anti-AS effects, reduced trimethylamine N-oxide levels from 349.9 to 189.2 ng/mL, and reduced aortic lipid deposition from 31.7 % to 9.5 %. AGOs significantly increased the levels of short-chain fatty acids in feces, in which acetic, propionic, and butyric acids were increased from 1.580, 0.364, and 0.469 mg/g to 2.233, 0.774, and 0.881 mg/g, respectively. An analysis of the gut microbiota indicated that AGOs restored alpha and beta diversity, decreased the Firmicutes/Bacteroidetes ratio, and promoted the dominance of the genus Akkermansia. A metagenomic analysis revealed that AGOs alleviated AS through the ABC transporter pathway and the lipopolysaccharide biosynthesis pathway.},
}
@article {pmid39326073,
year = {2024},
author = {Dong, S and Feng, H and Du, Y and Zhou, J and Xu, J and Lin, D and Ding, D and Xia, Y and Wang, M and Ding, Y},
title = {Source elimination of antibiotic resistance risk in aquaculture water by VUV/sulfite pretreatment.},
journal = {Journal of environmental management},
volume = {370},
number = {},
pages = {122644},
doi = {10.1016/j.jenvman.2024.122644},
pmid = {39326073},
issn = {1095-8630},
abstract = {Antibiotic resistance risk in the aquaculture industry is increasing with the excessive consumption of antibiotics. Although various efficient technologies for the degradation of antibiotics are available, the potential risk from antibiotic resistance in treated waters is often overlooked. This study compared the risks of antibiotic resistance in anaerobic sludge fed with pretreated florfenicol (FLO) containing wastewater after four UV or vacuum UV (VUV)-driven ((V)UV-driven) pretreatments, and established the VUV/sulfite recirculating water system to validate the effect of controlling the antibiotic resistance risk in the actual aquaculture water. Metagenomics sequencing revealed that a remarkable decrease in the abundance of antibiotic resistance genes (ARGs) was observed in four different pretreated groups, and results among the four pretreated groups were sorted in descending order based on ARG abundance: UV > VUV > UV/sulfite > VUV/sulfite. The low abundance of ARGs from VUV/sulfite group was close to that in the CK group (wastewater without FLO and without any pretreatments), which was 0.41 copies/cell. From the perspective of the temporal changes in the relative abundance of floR, the abundance in VUV/sulfite group remained lower than 11.67 ± 0.73 during the cultivation time. Additionally, microbial diversity analysis found that Proteobacteria and Firmicutes were major carriers of ARGs. Two species from Burkholderiaceae and Rhodocyclales were identified as potential co-hosts to spread by the correlation analysis of the abundances between floR or intI1 and the top 50 genera. Finally, the abundances of ARGs and MGEs in the VUV/sulfite recirculating water system with actual aquaculture water were reduced by 39.15% and 46.04%, respectively, compared to that in the blank group without any pretreatment. This study verified that VUV/sulfite pretreatment system could effectively control the antibiotic resistance risk of ARGs proliferation and transfer in aquaculture water. Furthermore, the study demonstrated that the reduction of antibiotic antibacterial activity plays an important role in the source control of resistance risk.},
}
@article {pmid39325867,
year = {2024},
author = {Fan, K and Cheng, Y and Hao, S},
title = {Lymph Node Histology and Metagenomic Sequencing in a child with Cat Scratch Disease.},
journal = {QJM : monthly journal of the Association of Physicians},
volume = {},
number = {},
pages = {},
doi = {10.1093/qjmed/hcae188},
pmid = {39325867},
issn = {1460-2393},
abstract = {A 4-year-old boy presented with fever and lymphadenopathy. Despite antibiotic treatment for suspected lymphadenitis, there was minimal improvement. A lymph node biopsy revealed granulomas, raising suspicion of cat scratch disease (CSD). The boy had been scratched by a kitten a month prior. Metagenomic testing of the tissue confirmed the presence of Bartonella henselae, the causative agent of CSD. It is important to incorporate molecular diagnostic tools into clinical practice for precise and timely diagnosis of infectious diseases.},
}
@article {pmid39325235,
year = {2024},
author = {Xing, S and Zhang, Z and Liu, C and Zhang, W and Zhang, Z and Tang, X and Chen, Y and He, W and Zhao, X and An, Y},
title = {Characteristics of Endemic Mycoses Talaromyces marneffei Infection Associated with Inborn Errors of Immunity.},
journal = {Journal of clinical immunology},
volume = {45},
number = {1},
pages = {17},
pmid = {39325235},
issn = {1573-2592},
support = {82070135//National Natural Science Foundation of China/ ; 2021YFC2700804//National Key R&amp;D Program of China/ ; W0100//CQMU Program for Youth Innovation in Future Medicine/ ; },
mesh = {Humans ; *Talaromyces ; *Mycoses/diagnosis/immunology ; Endemic Diseases ; Antifungal Agents/therapeutic use ; Genotype ; Immunologic Deficiency Syndromes/complications/diagnosis ; Opportunistic Infections/immunology/diagnosis ; },
abstract = {BACKGROUND: Talaromyces marneffei (T. marneffei) is an opportunistic pathogen that causes endemic mycoses, which could lead to multiple organ damage. Talaromycosis is frequently disregarded as an early cautionary sign of immune system disorders in non-HIV-infected children.<br><br>OBJECTIVE: We conduct a comprehensive review of the genotypes and clinical features of talaromycosis in patients with IEI to enhance clinical awareness regarding T. marneffei as a potential opportunistic pathogen in individuals with immune deficiencies.<br><br>METHODS: A systematic literature review was performed by searching PubMed, Cochrane Central Register of Controlled Trials, Web of Science, EMBASE, and Scopus. Data on IEI patients with talaromycosis, including genotypes and their immunological and clinical features, were collected.<br><br>RESULTS: Fifty patients with talaromycosis and IEI were included: XHIM (30.0%), STAT3-LOF deficiency (20.0%), STAT1-GOF (20.0%), IL2RG (6.00%), IFNGR1 (6.0%), IL12RB1 (4.0%), CARD9 (4.0%), COPA (4.0%), ADA (2.0%), RELB deficiency (2.0%), and NFKB2 (2.0%). Common symptoms of respiratory (43/50, 86.0%), skin (17/50, 34.0%), lymph node (31/50, 62.0%), digestive (34/50, 68.0%), and hematologic (22/50, 44.0%) systems were involved. The CT findings of the lungs may include lymph node calcification (9/30), interstitial lesions (8/30), pulmonary cavities (8/30), or specific pathogens (4/30), which could be easily misdiagnosed as tuberculosis infection. Amphotericin B (26/43), Voriconazole (24/43) and Itraconazole (22/43) were used for induction therapy. Ten patients were treated with Itraconazole sequentially and prophylaxis. 68.0% (34/50) of patients were still alive, and 4.0% (2/50) of were lost to follow-up. The disseminated T. marneffei infection resulted in the deaths of 14 individuals.<br><br>CONCLUSIONS: The XHIM, STAT1-GOF, and STAT3-LOF demonstrated the highest susceptibility to talaromycosis, indicating the potential involvement of cellular immunity, IL-17 signaling, and the IL-12/IFN-&#x3b3; axis in T. marneffei defense. T. marneffei infection may serve as an early warning indicator of IEI. For IEI patients suspected of T. marneffei, metagenomic next-generation sequencing (mNGS) could rapidly and effectively identify the causative pathogen. Prompt initiation of antifungal therapy is crucial for optimizing patient outcomes.},
}
@article {pmid39324818,
year = {2024},
author = {Li, F and Jia, M and Chen, H and Chen, M and Su, R and Usman, S and Ding, Z and Hao, L and Franco, M and Guo, X},
title = {Responses of microbial community composition and CAZymes encoding gene enrichment in ensiled Elymus nutans to altitudinal gradients in alpine region.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0098624},
doi = {10.1128/aem.00986-24},
pmid = {39324818},
issn = {1098-5336},
abstract = {UNLABELLED: High-throughput metagenomic sequence technology was employed to evaluate changes in microbial community composition and carbohydrate-active enzymes encoding gene enrichment status in Elymus nutans silages to altitudinal gradients in the world's highest alpine region of Qinghai-Tibetan Plateau (QTP). E. nutans were collected from three different altitudes in QTP: 2,600 m (low altitude), 3600 m (moderate altitude), and 4,600 m [high (H) altitude], and ensiled for 7, 14, 30, and 60 d. Results indicated an improvement in silage quality with the increasing altitude, although the acetic acid concentration and dry matter loss were greater in H altitude silages after 30 d of ensiling. Harmful bacteria or potential pathogens predominated in the microbial community on d 7 and 14 of fermentation, while genera belonging to lactic acid bacteria gradually became the main microorganisms with the increasing altitude on d 30 and 60 of ensiling. The abundance of carbohydrate-active enzymes genes responsible for macromolecular carbohydrate degradation in silage increased with increasing altitude, and those genes were mainly carried by Lactiplantibacillus and Pediococcus at 30 and 60 d of ensiling. The abundance of key enzymatic genes associated with glycolysis and organic acid production in carbohydrate metabolism pathway was higher in H altitude silages, and Lactiplantibacillus and Pediococcus were also the main hosts after 30 d of silage fermentation, except for the fact that acetic acid production was also related to genera Leuconostoc, Latilactobacillus, and Levilactobacillus.<br><br>IMPORTANCE: The fermentation quality of Elymus nutans silage was getting better with the increase of altitude in the Qinghai-Tibetan Plateau. The abundance of hosts carrying carbohydrate-active enzymes genes and key enzyme genes related to organic acid production increased with increasing altitude during the later stages of fermentation. Lactiplantibacillus and Pediococcus were the core microorganisms responsible for both polysaccharide hydrolysis and silage fermentation in the late stage of ensiling. This study provided insights on the influence of different altitudes on the composition and function of silage microbiome in the Qinghai-Tibetan Plateau, and provided a reference approach for improving the quality and controllability of silage production in high altitude areas of the Qinghai-Tibetan Plateau.},
}
@article {pmid39324627,
year = {2024},
author = {Bigatton, ED and Verdenelli, RA and Haro, RJ and Ayoub, I and Barbero, FM and Martín, MP and Dubini, LE and Jorrín Novo, JV and Lucini, EI and Castillejo, M&#xc1;},
title = {Metagenomic Analysis to Assess the Impact of Plant Growth-Promoting Rhizobacteria on Peanut (Arachis hypogaea L.) Crop Production and Soil Enzymes and Microbial Diversity.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.4c05687},
pmid = {39324627},
issn = {1520-5118},
abstract = {Peanut production could be increased through plant growth-promoting rhizobacteria (PGPR). In this regard, the present field research aimed at elucidating the impact of PGPR on peanut yield, soil enzyme activity, microbial diversity, and structure. Three PGPR strains (Bacillus velezensis, RI3; Bacillus velezensis, SC6; Pseudomonas psychrophila, P10) were evaluated, along with Bradyrhizobium japonicum (BJ), taken as a control. PGPR increased seed yield by 8%, improving the radiation use efficiency (4-14%). PGPR modified soil enzymes (fluorescein diacetate activity by 17% and dehydrogenase activity by 28%) and microbial abundance (12%). However, PGPR did not significantly alter microbial diversity; nonetheless, it modified the relative abundance of key phyla (Actinobacteria > Proteobacteria > Firmicutes) and genera (Bacillus > Arthrobacter > Pseudomonas). PGPRs modified the relative abundance of genes associated with N-fixation and nitrification while increasing genes related to N-assimilation and N-availability. PGPR improved agronomic traits without altering rhizosphere diversity.},
}
@article {pmid39324179,
year = {2024},
author = {Wu, X and Qi, T and Zhang, M and Bi, J},
title = {A rare case report of Prevotella lung abscess diagnosed using third-generation metagenomic sequencing.},
journal = {The Journal of international medical research},
volume = {52},
number = {9},
pages = {3000605241271757},
doi = {10.1177/03000605241271757},
pmid = {39324179},
issn = {1473-2300},
mesh = {Humans ; *Prevotella/isolation &amp; purification/genetics ; *Lung Abscess/microbiology/diagnosis ; *Metagenomics/methods ; Bacteroidaceae Infections/diagnosis/microbiology ; High-Throughput Nucleotide Sequencing/methods ; Female ; Male ; Tomography, X-Ray Computed ; },
abstract = {The Prevotella genus consists of obligate anaerobic Gram-negative bacteria that are symbiotic with the oral, intestinal, and vaginal mucosa. While several species of Prevotella have been implicated in pulmonary infections, identification of Prevotella as the causative agent of lung abscess is uncommon because of the requirement for stringent anaerobic culture conditions. In this report, we highlight a case of lung abscess caused by Prevotella salivae and Prevotella veroralis, underscoring the importance of third-generation metagenomic sequencing using devices from Oxford Nanopore Technologies for the precise diagnosis of specific pathogens.},
}
@article {pmid39323466,
year = {2024},
author = {Chen, L and Pei, M and Wang, X and Zhang, Y and Ma, Y and Chen, Y and Ahmad, I},
title = {Analysis of a case report of meningitis caused by Listeria monocytogenes.},
journal = {Frontiers in medicine},
volume = {11},
number = {},
pages = {1440225},
pmid = {39323466},
issn = {2296-858X},
abstract = {BACKGROUND: Listeria monocytogenes is a Gram-positive bacterium transmitted to humans through contaminated food, water, and animal faeces, posing a public health risk. Listeria monocytogenes is difficult to isolate and is not sensitive to first-line treatment with broad-spectrum cephalosporins for bacterial meningitis. Listeria meningitis is rare but can progress rapidly and may be accompanied by serious complications (hydrocephalus, ventricular inflammation, cerebral palsy, and brain abscess) and a high mortality rate.<br><br>CASE PRESENTATION: It is a retrospective analysis of the clinical characteristics and treatment of a rare case of Listeria monocytogenes infection. Using laboratory indicators such as white blood cells (WBC), C-reactive protein (CRP), and procalcitonin (PCT), three detection methods (cerebrospinal fluid/blood culture), Targeted gene sequencing technology (tNGS), and Metagenomic next-generation sequencing technology (mNGS) combined with clinical manifestations of patients, analyze the use plan and prognosis of antibiotics in patients. The patient in this case initially had neurological symptoms such as fever, headache, unclear consciousness, and vomiting; laboratory indicators include elevated WBC, CRP, and PCT. Listeria monocytogenes was cultured in both the patient's cerebrospinal fluid and blood samples. After treatment with penicillin and meropenem, the patient recovered and was discharged without any sequelae.<br><br>CONCLUSION: Due to the rarity of Listeria monocytogenes, there may be deficiencies and difficulties in clinical differential diagnosis, making it difficult to achieve targeted antibiotic treatment. Therefore, accurate identification of Listeria monocytogenes and relevant laboratory inflammation indicator testing, combined with traditional culture methods and NGS testing, through empirical coverage of Listeria monocytogenes, targeted antibiotic treatment ultimately impacts clinical outcomes significantly.},
}
@article {pmid39323103,
year = {2024},
author = {Abdisa, E and Esmaeily, M and Kwon, J and Jin, G and Kim, Y},
title = {A Nematode Isolate, Oscheius Tipulae, Exhibiting a Wide Entomopathogenic Spectrum and its Application to Control Dipteran Insect Pests.},
journal = {Archives of insect biochemistry and physiology},
volume = {117},
number = {1},
pages = {e22152},
doi = {10.1002/arch.22152},
pmid = {39323103},
issn = {1520-6327},
support = {//This work was supported by a grant (No. 2022R1A2B5B03001792) from the National Research Foundation (NRF) funded by the Minifistry of Science, ICT and Future Planning, Republic of Korea. This study was also funded by a research grant from Andong National University./ ; },
mesh = {Animals ; *Diptera/microbiology ; Pest Control, Biological ; Rhabditida/pathogenicity/physiology ; Virulence ; Symbiosis ; Nematoda ; Xenorhabdus/genetics/pathogenicity/physiology ; },
abstract = {An entomopathogenic nematode, Oscheius tipulae, was isolated from a soil sample. The identification of this species was supported by morphological and molecular markers. The nematode isolate exhibited pathogenicity against different target insects including lepidopteran, coleopteran, and dipteran insects. The virulence of this nematode was similar to that of a well-known entomopathogenic nematode, Steinernema carpocapsae, against the same insect targets. A comparative metagenomics analysis of these two nematode species predicted the existence of a combined total of 272 bacterial species in their intestines, of which 51 bacterial species were shared between the two nematode species. In particular, the common gut bacteria included several entomopathogenic bacteria including Xenorhabdus nematophila, which is known as a symbiotic bacterium to S. carpocapsae. The nematode virulence of O. tipulae to insects was enhanced by an addition of dexamethasone but suppressed by an addition of arachidonic acid, suggesting that the immune defenses of the target insects against the nematode infection is mediated by eicosanoids, which would be manipulated by the symbiotic bacteria of the nematode. Unlike S. carpocapsae, O. tipulae showed high virulence against dipteran insects including fruit flies, onion flies, and mosquitoes. O. tipulae showed particularly high control efficacies against the onion maggot, Delia platura, infesting the Welsh onion in the rhizosphere in both pot and field assays.},
}
@article {pmid39322959,
year = {2024},
author = {Wirbel, J and Essex, M and Forslund, SK and Zeller, G},
title = {A realistic benchmark for differential abundance testing and confounder adjustment in human microbiome studies.},
journal = {Genome biology},
volume = {25},
number = {1},
pages = {247},
pmid = {39322959},
issn = {1474-760X},
mesh = {Humans ; *Microbiota ; *Benchmarking ; RNA, Ribosomal, 16S/genetics ; Computer Simulation ; },
abstract = {BACKGROUND: In microbiome disease association studies, it is a fundamental task to test which microbes differ in their abundance between groups. Yet, consensus on suitable or optimal statistical methods for differential abundance testing is lacking, and it remains unexplored how these cope with confounding. Previous differential abundance benchmarks relying on simulated datasets did not quantitatively evaluate the similarity to real data, which undermines their recommendations.<br><br>RESULTS: Our simulation framework implants calibrated signals into real taxonomic profiles, including signals mimicking confounders. Using several whole&#xa0;meta-genome and 16S rRNA gene amplicon datasets, we validate that our simulated data resembles real data from disease association studies much more than in previous benchmarks. With extensively parametrized simulations, we benchmark the performance of nineteen differential abundance methods and further evaluate the best ones on confounded simulations. Only classic statistical methods (linear models, the Wilcoxon test, t-test), limma, and fastANCOM properly control false discoveries at relatively high sensitivity. When additionally considering confounders, these issues are exacerbated, but we find that adjusted differential abundance testing can effectively mitigate them. In a large cardiometabolic disease dataset, we showcase that failure to account for covariates such as medication causes spurious association in real-world applications.<br><br>CONCLUSIONS: Tight error control is critical for microbiome association studies. The unsatisfactory performance of many differential abundance methods and the persistent danger of unchecked confounding suggest these contribute to a lack of reproducibility among such studies. We have open-sourced our simulation and benchmarking software to foster a much-needed consolidation of statistical methodology for microbiome research.},
}
@article {pmid39322164,
year = {2024},
author = {Gao, YY and Zhou, YH and Liu, XP and Di, B and He, JY and Wang, YT and Guo, PT and Zhang, J and Wang, CK and Jin, L},
title = {Ganoderma lucidum polysaccharide promotes broiler health by regulating lipid metabolism, antioxidants, and intestinal microflora.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {135918},
doi = {10.1016/j.ijbiomac.2024.135918},
pmid = {39322164},
issn = {1879-0003},
abstract = {Ganoderma lucidum polysaccharides (GLP) are the primary bioactive macromolecular compounds of Ganoderma lucidum, possessing antioxidant and immunomodulatory effects. Hot water extract of Juncao-substrate Ganoderma Lucidum residue (HWE-JGLR) is abundant in GLP. There are few research reports on the application of HWE-JGLR in animal husbandry. Therefore, this study aims to investigate the effects of HWE-JGLR supplementation on growth performance, serum biochemistry, the antioxidant function of serum and liver, and the intestinal microbiota of yellow-feathered broilers. The control group was fed a corn-soybean meal basal diet, while the HJ I, II, and III groups received diets supplemented with 0.25 %, 0.5 %, and 1 % of HWE-JGLR, respectively. Results showed that HWE-JGLR increased the serum HDL-C content and decreased the TG content in broilers. Moreover, HWE-JGLR enhanced the antioxidant function by the Keap1-Nrf2/ARE signaling pathway and the antioxidative enzyme in broilers. In addition, the cecum of the metagenomic analysis of 16S rRNA showed that the relative abundance of no-rank Ruminococcacea was increased in the HJ I group. Our findings indicate that HWE-JGLR has strong potential for development as a green feed additive based on its functions of lipid-lowering, antioxidation, and the modulation of gut microbiota composition.},
}
@article {pmid39322110,
year = {2024},
author = {Liu, K and Li, Y and Ge, Z and Huang, D and Zhang, J},
title = {Microbial communities and mobile genetic elements determine the variations of antibiotic resistance genes for a continuous year in the urban river deciphered by metagenome assembly.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {125018},
doi = {10.1016/j.envpol.2024.125018},
pmid = {39322110},
issn = {1873-6424},
abstract = {Antibiotic resistance genes (ARGs) have become emerging environmental contaminants influenced by intricate regulatory factors. However, there is a lack of comprehensive studies on the evolution and distribution of ARGs over a full year in urban rivers, which serve as significant reservoirs of ARGs due to dynamic human activities. In this study, we conducted a 12-month metagenomic assembly to explore the microbial communities, ARGs, mobile genetic elements (MGEs) coexisting with ARGs, ARGs hosts, and the impact of environmental factors. Bacitracin (32%-47%) and multidrug (13%-24%) were detected throughout the year, constituting over 60% of the total abundance, making them the primary ARGs types. The assembly mechanisms of microbial communities and ARGs were primarily driven by stochastic processes. Integrase, IntI1, recombinase, and transposase were identified as the main MGEs coexisting with ARGs. Procrustes analysis revealed a significant structural association, indicating that the composition of host communities likely plays crucial roles in the seasonal composition and distribution of ARGs. Human pathogenic bacteria (HPBs) were identified in the summer, autumn, and winter, with Escherichia coli, Klebsiella pneumoniae, Acinetobacter lwoffii, and Burkholderiales bacterium being the primary HPBs. Mantle tests and PLS-PM equation analysis indicated that microbial communities and MGEs are the most critical factors determining the distribution and composition of ARGs in the river. Environmental factors (including water properties and nutrients) and ARGs hosts influence the evolution and abundance of ARGs by directly regulating microbial communities and MGEs. This study provides critical insights into risk assessment and management of ARGs in urban rivers.},
}
@article {pmid39322056,
year = {2024},
author = {Chen, J and Lin, Y and Zhu, Y and Zhang, Y and Qian, Q and Chen, C and Xie, S},
title = {Spatiotemporal profiles and underlying mechanisms of the antibiotic resistome in two water-diversion lakes.},
journal = {Environmental research},
volume = {},
number = {},
pages = {120051},
doi = {10.1016/j.envres.2024.120051},
pmid = {39322056},
issn = {1096-0953},
abstract = {Human-induced interventions have altered the local characteristics of the lake ecosystems through changes in hydraulic exchange, which in turn impacts the ecological processes of antibiotic resistance genes (ARGs) in the lakes. However, the current understanding of the spatiotemporal patterns and driving factors of ARGs in water-diversion lakes is still seriously insufficient. In the present study, we investigated antibiotic resistome in the main regulation and storage hubs, namely Nansi Lake and Dongping Lake, of the eastern part of the South-to-North Water Diversion project in Shandong Province (China) using a metagenomic-based approach. A total of 653 ARG subtypes belonging to 25 ARG types were detected with a total abundance of 0.125-0.390 copies/cell, with the dominance of bacitracin, multidrug, and macrolide-lincosamide streptogramin resistance genes. The ARG compositions were sensitive to seasonal variation and also interfered by artificial regulation structures along the way. Human pathogenic bacteria such as Acinetobacter calcoaceticus, Acinetobacter lwoffii, Klebsiella pneumoniae, along with the multidrug resistance genes they carried, were the focus of risk control in the two studied lakes, especially in summer. Plasmids were the key mobile genetic elements (MGEs) driving the horizontal gene transfer of ARGs, especially multidrug and sulfonamide resistance genes. The null model revealed that stochastic process was the main driver of ecological drift for ARGs in the lakes. The partial least squares structural equation model further determined that seasonal changes of pH and temperature drove a shift in the bacterial community, which in turn shaped the profile of ARGs by altering the composition of MGEs, antibacterial biocide- and metal-resistance genes (BMGs), and virulence factor genes (VFGs). Our results highlighted the importance of seasonal factors in determining the water transfer period. These findings can aid in a deeper understanding of the spatiotemporal variations of ARGs in lakes and their driving factors, offering a scientific basis for antibiotic resistance management.},
}
@article {pmid39321940,
year = {2024},
author = {Wang, P and Li, L and Zhang, Y and Ren, D and Feng, Y and Li, X and Wu, D and Xie, B and Ma, J},
title = {Triclosan facilitates the dissemination of antibiotic resistance genes during anaerobic digestion: Focusing on horizontal transfer and microbial response.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {131522},
doi = {10.1016/j.biortech.2024.131522},
pmid = {39321940},
issn = {1873-2976},
abstract = {The present study aims to investigate the mechanism by which triclosan influences the dissemination of antibiotic resistance genes (ARGs) during the whole anaerobic digestion process. qPCR and metagenomic analyses revealed that triclosan facilitated ARGs dissemination in a dose- and time-dependent manner. Furthermore, integrons exhibited a significant correlation with the majority of quantified ARGs, and various ARGs were frequently linked on integron gene cassettes. Microbial community and redundancy analyses indicated that triclosan altered the components of dominant ARGs hosts Firmicutes, Synergistetes and Bacteroidetes. Path modeling analysis confirmed integrons was the main driving force for facilitating ARGs dissemination. The promoted ARGs dissemination may be associated with the increased reactive oxygen species generation, cell membrane permeability, close-connected the ARGs transfer related regulatory proteins induced by triclosan. This study broadens the understanding of triclosan facilitates ARGs dissemination through anaerobic treatment, the strategies for preventing potential risks should be proposed in practice.},
}
@article {pmid39321483,
year = {2024},
author = {Vinyes-Nadal, M and Kümmel, S and Espín, Y and Gómez-Alday, JJ and Gehre, M and Otero, N and Torrentó, C},
title = {Dual C and Cl compound-specific isotope analysis and metagenomic insights into the degradation of the pesticide methoxychlor.},
journal = {Journal of hazardous materials},
volume = {480},
number = {},
pages = {135929},
doi = {10.1016/j.jhazmat.2024.135929},
pmid = {39321483},
issn = {1873-3336},
abstract = {This study investigates the use of multi-element compound-specific isotope analysis (ME-CSIA) to monitor degradation processes of methoxychlor, a persistent organochlorine insecticide. Laboratory experiments examined the kinetics, release of transformation products, and carbon and chlorine isotope effects during methoxychlor degradation through alkaline hydrolysis, oxidation with alkaline-activated persulfate, and biotic reductive dechlorination. Results showed that hydrolysis and oxidation did not cause significant carbon and chlorine isotope fractionation, indicating that C-H rather than C-Cl bond cleavage was the rate-determining step. Conversely, biotic reductive dechlorination by a field-derived microcosm under strictly anoxic conditions displayed significant carbon (εC = -0.9 ± 0.3 ‰) and chlorine (εCl = -1.9 ± 1.0 ‰) isotope fractionation. Its corresponding calculated dual isotope slope (ΛC/Cl = 0.4 ± 0.1) and apparent kinetic isotope effects (AKIEC = 1.014 ± 0.005 and AKIECl = 1.006 ± 0.003) indicate a C-Cl bond cleavage as the rate-determining step, highlighting the difference with respect to the other studied degradation mechanisms. Changes in the microbial community diversity revealed that families such as Dojkabacteria, Anaerolineaceae, Dysgonomonadaceae, Bacteroidetes vadinHA17, Pseudomonadaceae, and Spirochaetaceae, may be potential agents of methoxychlor reductive dechlorination under anoxic conditions. This study advances the understanding of degradation mechanisms of methoxychlor and improves the ability to track its transformation in contaminated environments, including for the first time an isotopic perspective.},
}
@article {pmid39320990,
year = {2024},
author = {Mian, E and Petrucci, E and Pizzi, C and Comin, M},
title = {MISSH: Fast Hashing of Multiple Spaced Seeds.},
journal = {IEEE/ACM transactions on computational biology and bioinformatics},
volume = {PP},
number = {},
pages = {},
doi = {10.1109/TCBB.2024.3467368},
pmid = {39320990},
issn = {1557-9964},
abstract = {Alignment-free analysis of sequences has revolutionized the high-throughput processing of sequencing data within numerous bioinformatics pipelines. Hashing k-mers represents a common function across various alignment-free applications, serving as a crucial tool for indexing, querying, and rapid similarity searching. More recently, spaced seeds, a specialized pattern that accommodates errors or mutations, have become a standard choice over traditional k-mers. Spaced seeds offer enhanced sensitivity in many applications when compared to k-mers. However, it's important to note that hashing spaced seeds significantly increases computational time. Furthermore, if multiple spaced seeds are employed, accuracy can be further improved, albeit at the expense of longer processing times. This paper addresses the challenge of efficiently hashing multiple spaced seeds. The proposed algorithms leverage the similarity of adjacent spaced seed hash values within an input sequence, allowing for the swift computation of subsequent hashes. Our experimental results, conducted across various tests, demonstrate a remarkable performance improvement over previously suggested algorithms, with potential speedups of up to 20 times. Additionally, we apply these efficient spaced seed hashing algorithms to a metagenomic application, specifically the classification of reads using Clark-S [Ounit and Lonardi, 2016]. Our findings reveal a substantial speedup, effectively mitigating the slowdown caused by the utilization of multiple spaced seeds.},
}
@article {pmid39320471,
year = {2024},
author = {Zou, W and Zhang, J and Li, Y and Zhang, Z and Yang, R and Yan, Y and Zhu, W and Ma, F and Jiang, P and Wang, Y and Zhang, X and Chen, J},
title = {Interstitial lung disease presents with varying characteristics in patients with non-Hodgkin lymphoma undergoing rituximab-containing therapies.},
journal = {Annals of hematology},
volume = {},
number = {},
pages = {},
pmid = {39320471},
issn = {1432-0584},
abstract = {Although the incidence and outcomes of rituximab-induced interstitial lung disease (RILD) have been partially reported, there are no systematic studies on the characteristics and types of RILD. This study aimed to investigate the clinical characteristics, bronchoalveolar lavage (BAL) findings, and treatment course of RILD in patients with non-Hodgkin lymphoma. We retrospectively analyzed the data from 321 patients with non-Hodgkin lymphoma who developed RILD between 2020 and 2022. The extent, distribution, and radiologic patterns of interstitial lung disease were determined using high-resolution computed tomography of the chest. BAL was performed in 299 (93.1%) patients to determine cellular distribution patterns and identify pathogenic microorganisms using metagenomic next-generation sequencing. All patients received combination therapy, with cyclophosphamide, doxorubicin, vincristine, and prednisone being the most commonly administered regimens. The median time from treatment to RILD development was 1.7 months. In the 217 patients who underwent metagenomic next-generation sequencing, 179 pathogenic microorganisms were detected, including 77 (43.0%) bacteria, 45 (25.1%) viruses, 28 (15.6%) Pneumocystis jirovecii strains, 17 (9.5%) fungi, 6 (3.5%) Mycobacterium tuberculosis, and 6 (3.5%) atypical pathogens. All RILD diagnoses were based on multidisciplinary team discussions and compliance with international standards. In conclusion, RILD exhibits a range of radiological and BAL patterns, reflecting different interstitial lung disease types. The most common patterns of RILD are infectious lung disease, organizing pneumonia, and nonspecific interstitial pneumonia. These findings enhance the understanding of RILD in patients with non-Hodgkin lymphoma and serve as a reference for best management guidelines in these patients.},
}
@article {pmid39320367,
year = {2024},
author = {Kayser, E and He, F and Nixon, S and Howard-Varona, A and Lamelas, A and Martinez-Blanch, J and Chenoll, E and Davenport, GM and de Godoy, MRC},
title = {Effects of Supplementation of Live and Heat-treated Bifidobacterium animalis subspecies lactis CECT 8145 on Glycemic and Insulinemic Response, Fecal Microbiota, Systemic Biomarkers of Inflammation, and White Blood Cell Gene Expression of Adult Dogs.},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skae291},
pmid = {39320367},
issn = {1525-3163},
abstract = {The popularity of functional ingredients such as probiotics and postbiotics has increased as pet owners seek ways to improve the health quality and longevity of their pets. Limited research has been conducted regarding the use of probiotics and postbiotics and their effects on canine health. The objective of this study was to evaluate the effects of daily supplementation of Bifidobacterium animalis subsp. lactis CECT 8145, in both live probiotic (PRO) and heat-treated postbiotic (POST) forms, on fecal fermentative end-products and microbiome, insulin sensitivity, serum gut hormones, oxidative stress, inflammatory biomarkers, and white blood cell gene expression of adult dogs. Eighteen adult beagles and 18 adult English pointers were used in a double-blinded placebo controlled parallel group design, with 12 animals per group (6 English pointers and 6 beagles). The study began with a 60 d adaptation period followed by a 90 d period of daily supplementation with either PRO, POST, or placebo (maltodextrin; CON). Longitudinal assessment of body weight (BW), body condition score (BCS), and pelvic circumference (PC) did not differ among dietary supplements (P > 0.05). Throughout the experimental period, fecal scores did not differ (P > 0.05), however, fecal pH was lower (P = 0.0049) in the dogs fed POST compared with CON. A higher fecal concentration of propionate (P = 0.043) was observed in dogs fed PRO and POST when compared with CON. While PRO and POST supplementation was associated with changes in bacterial composition at the family and genus level, the overall richness and diversity of the microbiome was not significantly affected. Functional analysis of the metagenome also suggests that PRO and POST supplementation induced potentially beneficial changes in the abundance of pathways involved in pathogenicity, amino acid biosynthesis and DNA repair. No differences in glycemic or insulinemic responses were observed among the groups (P > 0.05). Dogs supplemented with PRO had a higher (P < 0.05) mean white blood cell leptin relative fold gene expression compared with groups POST and CON. Serum metabolites and complete blood cells counts were within normal ranges and all dogs remained healthy throughout the study. Together, these data suggest that the PRO and POST can safely be supplemented for dogs. Moreover, the results of this study support further investigation of the role of PRO and POST in supporting parameters related to gut health and hormonal regulation.},
}
@article {pmid39320101,
year = {2024},
author = {Xue, H and Wang, Y and Mei, C and Han, L and Lu, M and Li, X and Chen, T and Wang, F and Tang, X},
title = {Gut microbiome and serum metabolome alterations associated with lactose intolerance (LI): a case‒control study and paired-sample study based on the American Gut Project (AGP).},
journal = {mSystems},
volume = {},
number = {},
pages = {e0083924},
doi = {10.1128/msystems.00839-24},
pmid = {39320101},
issn = {2379-5077},
abstract = {UNLABELLED: Lactose intolerance (LI) is a prevalent condition characterized by gastrointestinal symptoms that arise following lactose consumption. Recent evidence suggests that the gut microbiome may influence lactose levels in the gut. However, there is limited understanding regarding the alterations in microbiota and metabolism between individuals with LI and non-LI. This study conducted a paired-sample investigation utilizing data from the American Gut Project (AGP) and performed metagenomic and untargeted metabolomic analyses in a Chinese cohort to explore the interaction between the gut microbiome and serum metabolites. In addition, fecal microbiota transplantation (FMT) experiments were conducted to further examine the impact of the LI-associated gut microbiome on inflammatory outcomes. We identified 14 microbial genera that significantly differed between LI and controls from AGP data. Using a machine learning approach, group separation was predicted based on seven species and nine metabolites in the Chinese cohort. Notably, increased levels of Escherichia coli in the LI group were negatively correlated with several metabolites, including PC (22:6/0:0), indole, and Lyso PC, while reduced levels of Faecalibacterium prausnitzii and Eubacterium rectale were positively correlated with indole and furazolidone. FMT-LI rats displayed visceral hypersensitivity and an altered gut microbiota composition compared to FMT-HC rats. Metagenomic and metabolomic analyses revealed an enrichment of MAPK signaling in LI, which was confirmed by FMT-LI rats showing higher expression of ERK and RAS, along with increased concentrations of proinflammatory cytokines. This study provides valuable insights into the disrupted microbial and metabolic traits associated with LI, emphasizing potential microbiome-based approaches for its prevention and treatment.<br><br>IMPORTANCE: Lactose intolerance (LI) is a prevalent condition characterized by gastrointestinal symptoms after lactose consumption due to a deficiency of lactase. There is limited understanding regarding the microbiota and metabolic alterations between individuals with LI and non-LI. This study represents the first exploration to investigate metagenomic and metabolomic signatures among subjects with lactose intolerance as far as our knowledge. We identified 14 microbial genera in the Western cohort and 7 microbial species, along with 9 circulating metabolites in the Chinese cohort, which significantly differed in LI patients. Metagenomic and metabolomic analyses revealed an enrichment of MAPK signaling in LI patients. This finding was confirmed by FMT-LI rats, exhibiting increased expression of ERK and RAS, along with higher concentrations of pro-inflammatory cytokines. Our study provides insights into the disrupted functional and metabolic traits of the gut microbiome in LI, highlighting potential microbiome-based approaches for preventing and treating LI.},
}
@article {pmid39319930,
year = {2024},
author = {Schuelter, AR and Pedron, LEC and Silva, GJD and Bonett, LP and Souza, IRP and Grignet, RS and Stathacos, JVG and Alves Netto, AF and Coelho, SRM},
title = {Metagenomics and vegetative growth of Salvia hispanica inoculated with Trichoderma harzianum.},
journal = {Brazilian journal of biology = Revista brasleira de biologia},
volume = {84},
number = {},
pages = {e284877},
doi = {10.1590/1519-6984.284877},
pmid = {39319930},
issn = {1678-4375},
mesh = {*Salvia/microbiology ; *Soil Microbiology ; *Metagenomics ; Rhizosphere ; Biomass ; Hypocreales/physiology ; Plant Roots/microbiology ; },
abstract = {The soil is a dynamic environment, influenced by abiotic and biotic factors, which can result in changes in plant development. This study aimed to assess the impact on vegetative growth of chia (Salvia hispanica L) inoculated with Trichoderma harzianum and on the rhizosphere microbiome. The experimentation was conducted in a greenhouse under controlled conditions growing chia plants in pots containing soil with a clayey texture. Different concentrations of T. harzianum (0; 2.5; 5.0; 10.0; 20.0 µL. g-1 of seed) were applied to the chia seeds before planting. Morphological parameters, including plant height (cm), number of branches, stem diameter (mm), number of days to flowering and shoot and root dry masses (g) were quantitatively assessed. After the cultivation period, soil samples from the rhizosphere region were collected for subsequent chemical and metagenomic analyses. These samples were also compared with the control soil, collected before installing the experiment. The results showed that increasing doses of T. harzianum promoted a significant increase in the diameter of the stem, number of branches, dry biomass of the root system and the number of days to flowering, without modifying the overall height of the plants. Soil metagenomics indicated that T. harzianum inoculation modified the microbial diversity of the rhizosphere environment, with more pronounced effects observed in samples treated with higher concentrations of the inoculant. Furthermore, there were changes in the chemical composition and enzymes related to soil quality in correlation with the concentrations of the applied inoculant. This study demonstrated that inoculating chia seeds with T. harzianum not only promotes specific morphogenetic characteristics of the plant, but it also has a significant impact on the microbial diversity and biochemical functionality of the soil, including an observed increase in the populations of T. harzianum and T. asperellum.},
}
@article {pmid39319624,
year = {2024},
author = {Shi, Q and Fu, Q and Zhang, J and Hao, G and Liang, C and Duan, F and Ma, J and Zhao, H and Song, W},
title = {Paenibacillus polymyxa J2-4 induces cucumber to enrich rhizospheric Pseudomonas and contributes to Meloidogyne incognita management under field conditions.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.8429},
pmid = {39319624},
issn = {1526-4998},
support = {2023YFD1400400//National Key R&amp;D Program of China/ ; 2022CXGC020710-6//Subproject of Shandong Province Key R&amp;D Plan Project/ ; QNYCX23027//Qingdao Agricultural University Graduate Student Innovation Program/ ; QNYCX24076//Qingdao Agricultural University Graduate Student Innovation Program/ ; },
abstract = {BACKGROUND: Root knot nematodes (RKNs) pose a great threat to agricultural production worldwide. The bacterial nematocides have received increasing attention due to their safe and efficient control against RKNs. Here, we investigated the biocontrol efficacy of Paenibacillus polymyxa J2-4 against Meloidogyne incognita in the field and analyzed the rhizosphere microbiome of cucumber under nematode infection after application of the J2-4 strain. Furthermore, a biomarker strain of Pseudomonas spp. was isolated from the J2-4-inoculated rhizosphere soil, and its nematocidal activity and growth-promoting effect on host plants were determined. In addition, chemotaxis assay of P. fluroescens ZJ5 toward root exudates was carried out.<br><br>RESULTS: The field experiment demonstrated that P. polymyxa J2-4 could effectively suppressed gall formation in cucumber plants, with the galling index reduced by 67.63% in 2022 and 65.50% in 2023, respectively, compared with controls. Meanwhile, plant height and yield were significantly increased in J2-4 treated plants compared with controls. Metagenomic analysis indicated that J2-4 altered the rhizosphere microbial communities. The relative abundance of Pseudomonas spp. was notably enhanced in the J2-4 group, which was consistent with Linear discriminant analysis Effect Size results that Pseudomonas was determined as one of the biomarkers in the J2-4 group. Furthermore, the ZJ5 strain, one of the biomarker Pseudomonas strains, was isolated from the J2-4-inoculated rhizosphere soil and was identified as Pseudomonas fluorescens. In addition, P. fluorescens ZJ5 exhibited high nematicidal activity in vitro and in vivo, with 99.20% of the mortality rate of M. incognita at 24&#x2009;h and 69.75% of gall index reduction. The biocontrol efficiency of the synthetic community of ZJ5 plus J2-4 was superior to that of any other single bacteria against M. incognita. Additionally, ZJ5 exhibited great chemotaxis ability toward root exudates inoculated with J2-4.<br><br>CONCLUSION: Paenibacillus polymyxa J2-4 has good potential in the biological control against M. incognita under field conditions. Enrichment of the beneficial bacteria Pseudomonas fluorescens ZJ5 in the J2-4-inoculated rhizosphere soil contributes to M. incognita management. &#xa9; 2024 Society of Chemical Industry.},
}
@article {pmid39318437,
year = {2024},
author = {Sharma, P and Pandey, R and Chauhan, NS},
title = {Unveiling wheat growth promotion potential of phosphate solubilizing Pantoea agglomerans PS1 and PS2 through genomic, physiological, and metagenomic characterizations.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1467082},
pmid = {39318437},
issn = {1664-302X},
abstract = {INTRODUCTION: Phosphorus is an abundant element in the earth's crust and is generally found as complex insoluble conjugates. Plants cannot assimilate insoluble phosphorus and require external supplementation as chemical fertilizers to achieve a good yield. Continuous use of fertilizers has impacted soil ecology, and a sustainable solution is needed to meet plant elemental requirements. Phosphate solubilizing microbes could enhance phosphorus bioavailability for better crop production and can be employed to attain sustainable agriculture practices.<br><br>METHODS: The current study unveils the biofertilizer potential of wheat rhizospheric bacteria through physiological, taxonomic, genomic, and microbiomics experimentations.<br><br>RESULTS AND DISCUSSION: Culture-dependent exploration identified phosphate-solubilizing PS1 and PS2 strains from the wheat rhizosphere. These isolates were rod-shaped, gram-negative, facultative anaerobic bacteria, having optimum growth at 37&#xb0;C and pH 7. Phylogenetic and phylogenomic characterization revealed their taxonomic affiliation as Pantoea agglomerans subspecies PS1 &amp; PS2. Both isolates exhibited good tolerance against saline (>10% NaCl (w/v), >11.0% KCl (w/v), and >6.0% LiCl (w/v)), oxidizing (>5.9% H2O2 (v/v)) conditions. PS1 and PS2 genomes harbor gene clusters for biofertilization features, root colonization, and stress tolerance. PS1 and PS2 showed nitrate reduction, phosphate solubilization, auxin production, and carbohydrate utilization properties. Treatment of seeds with PS1 and PS2 significantly enhanced seed germination percentage (p = 0.028 and p = 0.008, respectively), number of tillers (p = 0.0018), number of leaves (p = 0.0001), number of spikes (p = 0.0001) and grain production (p = 0.0001). Wheat rhizosphere microbiota characterizations indicated stable colonization of PS1 and PS2 strains in treated seeds at different feek stages. Pretreatment of seeds with both strains engineered the wheat rhizosphere microbiota by recruiting plant growth-promoting microbial groups. In vitro, In vivo, and microbiota characterization studies indicated the biofertilizer potential of Pantoea sp. PS1 &amp; PS2 to enhance wheat crop production. The employment of these strains could fulfill plant nutrient requirements and be a substitute for chemical fertilizers for sustainable agriculture.},
}
@article {pmid39318431,
year = {2024},
author = {Robinson, D and Morgan-Kiss, RM and Wang, Z and Takacs-Vesbach, C},
title = {Antarctic lake viromes reveal potential virus associated influences on nutrient cycling in ice-covered lakes.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1422941},
pmid = {39318431},
issn = {1664-302X},
abstract = {The McMurdo Dry Valleys (MDVs) of Antarctica are a mosaic of extreme habitats which are dominated by microbial life. The MDVs include glacial melt holes, streams, lakes, and soils, which are interconnected through the transfer of energy and flux of inorganic and organic material via wind and hydrology. For the first time, we provide new data on the viral community structure and function in the MDVs through metagenomics of the planktonic and benthic mat communities of Lakes Bonney and Fryxell. Viral taxonomic diversity was compared across lakes and ecological function was investigated by characterizing auxiliary metabolic genes (AMGs) and predicting viral hosts. Our data suggest that viral communities differed between the lakes and among sites: these differences were connected to microbial host communities. AMGs were associated with the potential augmentation of multiple biogeochemical processes in host, most notably with phosphorus acquisition, organic nitrogen acquisition, sulfur oxidation, and photosynthesis. Viral genome abundances containing AMGs differed between the lakes and microbial mats, indicating site specialization. Using procrustes analysis, we also identified significant coupling between viral and bacterial communities (p = 0.001). Finally, host predictions indicate viral host preference among the assembled viromes. Collectively, our data show that: (i) viruses are uniquely distributed through the McMurdo Dry Valley lakes, (ii) their AMGs can contribute to overcoming host nutrient limitation and, (iii) viral and bacterial MDV communities are tightly coupled.},
}
@article {pmid39318384,
year = {2024},
author = {Yin, C and Liu, L and Xu, D and Li, M and Li, M and Qin, Y and Zhang, B and Sun, Y and Liu, Y and Xiao, Y},
title = {Integrative metagenomic and lipidomic analyses reveal alterations in children with obesity and after lifestyle intervention.},
journal = {Frontiers in nutrition},
volume = {11},
number = {},
pages = {1423724},
pmid = {39318384},
issn = {2296-861X},
abstract = {BACKGROUND: Despite emerging evidence linking alterations in gut microbiota to childhood obesity, the metabolic mechanisms linking gut microbiota to the lipid profile during childhood obesity and weight loss remain poorly understood.<br><br>METHODOLOGY: In this study, children with obesity were treated with lifestyle weight loss therapy. Metagenomics association studies and serum untargeted lipidomics analyses were performed in children with obesity and healthy controls before and after weight loss.<br><br>MAIN FINDINGS: We identified alterations in gut microbiota associated with childhood obesity, as well as variations in circulating metabolite concentrations. Children with obesity showed significant decreases in the levels of s-Rothia_kristinae and s-Enterobacter_roggenkampii, alongsige elevated levels of s-Clostridiales_bacterium_Marseille-P5551. Following weight loss, the levels of s-Streptococcus_infantarius and s-Leuconostoc_citreum increased by factors of 3.354 and 1.505, respectively, in comparison to their pre-weight loss levels. Correlation analyses indicated a significant positive relationship between ChE(2:0) levels and both with s-Lachnospiraceae_bacterium_TF09-5 and fasting glucose levels. CoQ8 levels were significantly negatively correlated with s-Rothia_kristinae and HOMA-IR.<br><br>CONCLUSION: We linked altered gut microbiota and serum lipid levels in children with obesity to clinical indicators, indicating a potential impact on glucose metabolism via lipids. This study contributes to understanding the mechanistic relationship between altered gut microbiota and childhood obesity and weight loss, suggesting gut microbiome as a promising target for intervention.<br><br>CLINICAL TRIAL REGISTRATION: https://www.chictr.org.cn/showproj.html?proj=178971, ChiCTR2300072179.},
}
@article {pmid39317249,
year = {2024},
author = {Liu, YH and Huang, JN and Wen, B and Gao, JZ and Chen, ZZ},
title = {Comprehensive assessment of three crayfish culture modes: From production performance to environmental sustainability.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {176470},
doi = {10.1016/j.scitotenv.2024.176470},
pmid = {39317249},
issn = {1879-1026},
abstract = {Integrated agriculture-aquaculture has emerged as a promising ecological development model. Crayfish, a popular aquaculture species, are traditionally reared either in monoculture ponds (mono-C) or in rice-crayfish polyculture system (poly-RC). In this study, we introduced a novel polyculture system by combining fruit tree with crayfish (poly-FC), aiming to compare these three crayfish culture modes in terms of production performance and ecological sustainability. The results indicated that crayfish reared in the two polyculture modes exhibited significantly higher specific growth rate and condition factor compared to those in mono-C. Crayfish cultured in poly-FC also showed better muscle quality and higher levels of crude fat and flavor or essential amino acids. Isotope mixing model showed that feed and benthic animals were the primary food sources of crayfish in mono-C, whereas aquatic plants, fruit litter or rice contributed more to those in polyculture modes. For greenhouse gas emissions, poly-FC mode emitted almost no CO2 and N2O even favored negative CH4 emission, while poly-RC and mono-C modes showed positive emissions of CH4 and CO2, respectively. Supported by metagenomics, the sink of CH4 in poly-FC was probably due to the lower mcr abundance but the higher pmo abundance in water. The low production and emission of N2O in poly-FC might result from the low-abundant Nitrospirae_bacterium and its coding gene norC in sediment, consistent with the lower denitrification rate but the higher NO3[-] concentration than mono-C. Overall, our findings reveal the superiority of polyculture of fruit tree with crayfish in terms of production performance and greenhouse gas emissions in the system.},
}
@article {pmid39316987,
year = {2024},
author = {Yang, H and Liu, Y and Cao, G and Liu, J and Xiao, S and Xiao, P and Tao, Y and Gao, H},
title = {Effects of lycopene on the growth performance, meat quality, cecal metagenome, and hepatic untargeted metabolome in heat stressed broilers.},
journal = {Poultry science},
volume = {103},
number = {12},
pages = {104299},
doi = {10.1016/j.psj.2024.104299},
pmid = {39316987},
issn = {1525-3171},
abstract = {The occurrence of heat stress in poultry houses is inevitable and leads to oxidative stress in the birds. Lycopene, a natural hydrocarbon carotenoid, possesses potent antioxidant properties. This study aimed to investigate the impact of lycopene on growth performance, meat quality, cecal microflora, and liver metabolome in broilers subjected to heat stress. A total of 480 yellow feather broilers were randomly allocated into 4 treatment groups: birds fed standard diet (Con), birds fed standard diet and supplemented with lycopene (Lyc), birds fed standard diet and subjected to heat stress (Hs), and birds fed with lycopene and subjected to heat stress (Hs-Lyc). As compared with the normal temperature groups, Hs decreased the average daily gain (ADG) of birds during d 1 to 28, lowered the pH value either in breast meat or thigh meat, increased the L* value of breast meat, and decreased the a* value of thigh meat. In comparison with non-Lyc feeding birds, Lyc supplement elevated the ADG during d 1 to 56, increased the pH of breast meat, decrease the L* and b* values of thigh meat, simultaneously increase the a* value of thigh meat. The L* of breast meat and pH of thigh meat exhibited significant differences under Hs-Lyc treatment. Lyc-treated birds exhibited higher elasticity, gumminess, and resilience in breast meat than those in non-Lyc feeding birds. The cecal metagenome analysis indicated that Hs-Lyc treatment increased the abundance of Phocaeicola salanitronis and Prevotella sp.CAG:1058, Bacteroides sp.An269, and Bacteroides sp.An19 at the species level compared with other treatments. The hepatic untargeted metabolome analysis showed that administration of Lyc upregulated 20 metabolites and downregulated 60 metabolites compared to the Con birds. Futhermore, the Hs-Lyc treatment upregulated 34 metabolites and downregulated 45 metabolites compared to the Hs birds. The correlation between the metagenome and metabolome showed that Lyc supplementation induced significant alterations in the citrate cycle, metabolism of butanoate, glycolysis/gluconeogenesis, glyoxylate and dicarboxylate, alanine, aspartate, and glutamate compared with standard supplement. In contrast, Hs-Lyc treatment induced alterations in the citrate cycle, metabolism of pyruvate, glyoxylate, and dicarboxylate, glycolysis/gluconeogenesis, arginine, proline, alanine, aspartate, and glutamate compared with the standard supplement of heat-challenged broilers. In summary, dietary Lyc supplementation promoted the growth performance, changed the meat quality, modulated the cecal metagenome and hepatic metabolome in heat-stressed broilers.},
}
@article {pmid39316964,
year = {2024},
author = {Pi, K and Xie, X and Sun, S and Van Cappellen, P and Xiao, Z and Zhang, D and Wang, Y},
title = {Arsenic redox disequilibrium in geogenic contaminated groundwater: Bioenergetic insights from organic molecular characterization and gene-informed modeling.},
journal = {Water research},
volume = {267},
number = {},
pages = {122459},
doi = {10.1016/j.watres.2024.122459},
pmid = {39316964},
issn = {1879-2448},
abstract = {Biotransformation of arsenic (As) influences its speciation and mobility, obscuring mechanistic comprehension on spatiotemporal variation of As concentration in geogenic contaminated groundwater. In particular, unresolved processes underlying As redox disequilibrium in comparison to major redox couples discourage practical efforts to rehabilitate the As-contaminated groundwater. Here, quantitative metagenomic sequencing and ultrahigh-resolution mass spectrometry (FT-ICR-MS) were jointly applied to reveal the links between vertical distribution of As metabolic gene assemblages and that of free energy density of dissolved organic matter (DOM) in As-contaminated groundwater of Datong Basin. Observed small excess of Gibbs free energy available by DOM relative to that required for As(V)-to-As(III) reduction exerts thermodynamic constraint on metabolism-mediated redox transformation of As. Accordingly, the vertical distribution of dissolved As(V)/As(III) ratio correlated significantly with that of ars+acr3 and arr encoding As(V) reduction and aio encoding As(III) oxidation in the moderately/strongly reducing groundwater. Further gene-informed biogeochemical modeling suggests that a net effect of these kinetics-restricted bidirectional metabolic pathways leads to co-preservation of As(V) and As(III) even at relatively high rates of ars+acr3 encoded As(V) reduction. This study therefore provides new insights into bioenergetic constraints on As hydrobiogeochemical behavior, with implications for other redox-sensitive contaminants in the groundwater systems.},
}
@article {pmid39316963,
year = {2024},
author = {Ping, J and Dong, Y and Xie, L and Zhou, Y and Zhang, L and Huang, Y and Liao, L and Cheng, W and Peng, F and Song, H},
title = {Effect of reactive oxygen species (ROS) produced by pyridine and quinoline on NH4[+]-N removal under phenol stress: The shift of nitrification pathway and its potential mechanisms.},
journal = {Water research},
volume = {267},
number = {},
pages = {122478},
doi = {10.1016/j.watres.2024.122478},
pmid = {39316963},
issn = {1879-2448},
abstract = {Pyridine and quinoline are typical nitrogenous heterocyclic compounds with different structures that are found in coking wastewater. However, neither the corresponding mechanism nor its effect on the degradation of NH4[+]-N under phenol stress is known. In this study, the effects of pyridine and quinoline degradation on NH4[+]-N removal under phenol stress were evaluated using three lab-scale sequencing batch reactors. The average NH4[+]-N removal efficiencies of the reactors were 99.46 %, 88.86 %, and 98.64 %. With the increased concentration of pyridine and quinoline, NH4[+]-N and NO3[-]-N accumulated to 58.37 mg/L and 141.37 mg/L, respectively, due to the lack of an electron donor and anaerobic environment. The addition of pyridine and quinoline significantly improved antioxidant response and altered the nitrification pathway. The nitrification process shifted from the mediation of amo and hao to the mediation of Ncd2 due to oxidative stress induced by pyridine and quinoline. Furthermore, oxidative stress interferes with the metabolism of carbon sources, resulting in decreased biomass. These results provide a new perspective for coking wastewater treatment processes.},
}
@article {pmid39316685,
year = {2024},
author = {Ke, S and Gálvez, JAV and Sun, Z and Cao, Y and Pollock, NR and Chen, X and Kelly, CP and Liu, YY},
title = {Rational Design of Live Biotherapeutic Products for the Prevention of Clostridioides difficile Infection.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiae470},
pmid = {39316685},
issn = {1537-6613},
abstract = {Clostridioides difficile infection (CDI) is a major cause of healthcare- and antibiotic-associated diarrhea. While fecal microbiota transplantation (FMT) shows promise for recurrent CDI, its mechanisms and long-term safety are not fully understood. Live biotherapeutic products (LBPs) using pre-defined bacterial consortia offer an alternative option, but the rational designing LBPs remains challenging. Here, we employ a computational pipeline and three metagenomic datasets to identify microbial strains for LBPs targeting CDI. We constructed the CDI-related microbial genome catalog, comprising 3,741 non-redundant metagenome-assembled genomes (nrMAGs) and identified multiple potential protective nrMAGs, including strains from Dorea formicigenerans, Oscillibacter welbionis, and Faecalibacterium prausnitzii. Importantly, some of these protective nrMAGs were found to play an important role in FMT success, and most top protective nrMAGs can be validated by various previous findings. Our results demonstrate a framework for selecting microbial strains targeting CDI, paving the way for the computational design of LBPs against other enteric infections.},
}
@article {pmid39316448,
year = {2024},
author = {Wang, Y and Shi, YN and Xiang, H and Shi, YM},
title = {Exploring nature's battlefield: organismic interactions in the discovery of bioactive natural products.},
journal = {Natural product reports},
volume = {},
number = {},
pages = {},
doi = {10.1039/d4np00018h},
pmid = {39316448},
issn = {1460-4752},
abstract = {Covering: up to March 2024.Microbial natural products have historically been a cornerstone for the discovery of therapeutic agents. Advanced (meta)genome sequencing technologies have revealed that microbes harbor far greater biosynthetic capabilities than previously anticipated. However, despite the application of CRISPR/Cas-based gene editing and high-throughput technologies to activate silent biosynthetic gene clusters, the rapid identification of new natural products has not led to a proportional increase in the discovery rate of lead compounds or drugs. A crucial issue in this gap may be insufficient knowledge about the inherent biological and physiological functions of microbial natural products. Addressing this gap necessitates recognizing that the generation of functional natural products is deeply rooted in the interactions between the producing microbes and other (micro)organisms within their ecological contexts, an understanding that is essential for harnessing their potential therapeutic benefits. In this review, we highlight the discovery of functional microbial natural products from diverse niches, including those associated with humans, nematodes, insects, fungi, protozoa, plants, and marine animals. Many of these findings result from an organismic-interaction-guided strategy using multi-omic approaches. The current importance of this topic lies in its potential to advance drug discovery in an era marked by increasing antimicrobial resistance.},
}
@article {pmid39315852,
year = {2024},
author = {Tian, W and Tang, Y and Ducey, TF and Khan, E and Tsang, DCW},
title = {Facilitating Intracellular Electron Bifurcation by Mediating Flavin-Based Extracellular and Transmembrane Electron Transfer: A Novel Role of Pyrogenic Carbon in Dark Fermentation for Hydrogen Production.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c05994},
pmid = {39315852},
issn = {1520-5851},
abstract = {Pyrogenic carbon is considered an enhancer to H2-yielding dark fermentation (DF), but little is known about how it regulates extracellular electron transfer (EET) and influences transmembrane respiratory chains and intracellular metabolisms. This study addressed these knowledge gaps and demonstrated that wood waste pyrogenic carbon (biochar) could significantly improve the DF performance; e.g., addition of pyrogenic carbon produced by pyrolysis at 800 °C (PC800) increased H2 yield by 369.7%. Biochemical quantification, electrochemical analysis, and electron respiratory chain inhibition tests revealed that PC800 promoted the extracellular flavin-based electron transfer process and further activated the acceleration of the transmembrane electron transfer. Comparative metagenome/metatranscriptome analyses indicated that the flavin-containing Rnf complex was the potential transmembrane respiratory enzyme associated with PC800-mediated EET. Based on NADH/NAD[+] circulation, the promoted Rnf complex could stimulate the functions of the electron bifurcating Etf/Bcd complex and startup of glycolysis. The promoted Etf/Bcd could further contribute to balance the NADH/NAD[+] level for glycolytic reactions and meanwhile provide reduced ferredoxin for group A1 [FeFe]-hydrogenases. This proton-energy-linked mechanism could achieve coupling production of ATP and H2. This study verified the important roles of pyrogenic carbon in mediating EET and transmembrane/intracellular pathways and revealed the crucial roles of electron bifurcation in DF for hydrogen production.},
}
@article {pmid39315850,
year = {2024},
author = {Yao, G and Zhang, X and Zhang, T and Jin, J and Qin, Z and Ren, X and Wang, X and Zhang, S and Yin, X and Tian, Z and Zhang, Y and Zhang, J and Wang, Z and Zhang, Q},
title = {The role of dysbiotic gut mycobiota in modulating risk for abdominal aortic aneurysm.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0177624},
doi = {10.1128/spectrum.01776-24},
pmid = {39315850},
issn = {2165-0497},
abstract = {UNLABELLED: Abdominal aortic aneurysm (AAA) is a large-vessel disease with high mortality, characterized by complex pathogenic mechanisms. Current therapeutic approaches remain insufficient to halt its progression. Fungi are important members of the gut microbiota. However, their characteristic alterations and roles in AAA remain unclear. This study investigated the role of gut fungal communities in the development of AAA through metagenomic sequencing of fecal samples from 31 healthy individuals and 33 AAA patients. We observed significant dysbiosis in the gut mycobiomes of AAA patients compared to healthy individuals, characterized by an increase in pathogenic fungi like Candida species and a decrease in beneficial yeasts such as Saccharomyces cerevisiae. The changes in fungal populations correlated strongly with clinical indicators of AAA, highlighting their potential for diagnosing and predicting AAA progression. Furthermore, our animal experiments demonstrated that Saccharomyces cerevisiae significantly ameliorated pathological alterations in AAA mice, suggesting a protective role for specific yeast strains against AAA development. These findings underscore the significant impact of gut mycobiomes on AAA and suggest that modulating these fungal communities could offer a novel therapeutic approach. Our research advances the understanding of the influence of gut microbiome on vascular diseases and suggests potential non-surgical approaches for managing AAA. By elucidating the diagnostic and therapeutic potential of gut fungi in AAA, this study provided important clues for future clinical strategies and therapeutic developments in the field of vascular medicine.<br><br>IMPORTANCE: Our research highlights the crucial role of gut fungi in abdominal aortic aneurysm (AAA) development. By analyzing fecal samples from AAA patients and healthy controls, we discovered significant dysbiosis in gut fungal communities, characterized by an increase in harmful Candida species and a decrease in beneficial yeasts like Saccharomyces cerevisiae. This dysbiosis was correlated with the severity of AAA. Importantly, in animal experiments, supplementing with Saccharomyces cerevisiae significantly slowed AAA progression. These findings suggest that modulating gut fungi may offer a novel, non-surgical approach to the diagnosis and treatment of AAA, potentially reducing the need for invasive procedures.},
}
@article {pmid39315838,
year = {2024},
author = {Bulka, O and Edwards, EA},
title = {Two distinct Dehalobacter metagenome-assembled genomes from anaerobic chloroform and dichloromethane degrading consortia.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0080324},
doi = {10.1128/mra.00803-24},
pmid = {39315838},
issn = {2576-098X},
abstract = {Here we present two metagenomes and two Dehalobacter metagenome-assembled genomes from subcultures of an anaerobic chloroform and dichloromethane degrading microbial community used for bioremediation. Our objective was to assemble and curate the genome(s) of Dehalobacter, key biodegraders in the culture, through repeated sequencing and joint assembly with previous datasets.},
}
@article {pmid39315801,
year = {2024},
author = {Tenorio-Carnalla, K and Aguilar-Vera, A and Hernández-Alvarez, AJ and López-Leal, G and Mateo-Estrada, V and Santamaria, RI and Castillo-Ramírez, S},
title = {Host population structure and species resolution reveal prophage transmission dynamics.},
journal = {mBio},
volume = {},
number = {},
pages = {e0237724},
doi = {10.1128/mbio.02377-24},
pmid = {39315801},
issn = {2150-7511},
abstract = {UNLABELLED: Much knowledge about bacteriophages has been obtained via genomics and metagenomics over the last decades. However, most studies dealing with prophage diversity have rarely conducted phage species delimitation (aspect 1) and have hardly integrated the population structure of the host (aspect 2). Yet, these two aspects are essential in assessing phage diversity. Here, we implemented an operational definition of phage species (clustering at 95% identity, 90% coverage) and integrated the host's population structure to understand prophage diversity better. Gathering the most extensive data set of Acinetobacter baumannii phages (4,152 prophages + 122 virulent phages, distributed in 46 countries in the world), we show that 91% (875 out of 963) of the prophage species have four or fewer prophages per species, and just five prophage species have more than 100 prophages. Most prophage species have a narrow host range and are geographically restricted; yet, very few have a broad host range being well spread in distant lineages of A. baumannii. These few broad host range prophage species are not only cosmopolitan but also the most abundant species. We also noted that polylysogens had very divergent prophages, belonging to different prophage species, and prophages can easily be gained and lost within the bacterial lineages. Finally, even with this extensive data set, the prophage diversity has not been fully grasped. Our study highlights how integrating the host population structure and a solid operational definition of phage species allows us to better appreciate phage diversity and its transmission dynamics.<br><br>IMPORTANCE: Much knowledge about bacteriophages has been obtained via genomics and metagenomics over the last decades. However, most studies dealing with prophage diversity have rarely conducted phage species delimitation (aspect 1) and have hardly integrated the population structure of the host (aspect 2). Yet, these two aspects are essential in assessing phage diversity. Here, we implemented an operational definition of phage species (clustering at 95% identity, 90% coverage) and integrated the host's population structure to understand prophage diversity better. Gathering the most extensive data set of Acinetobacter baumannii phages, we show that most prophage species have four or fewer prophages per species, and just five prophage species have more than 100 prophages. Most prophage species have a narrow host range and are geographically restricted; yet, very few have a broad host range being well spread in distant lineages of A. baumannii. These few broad host range prophage species are cosmopolitan and the most abundant species. Prophages in the same bacterial genome are very divergent, and prophages can easily be gained and lost within the bacterial lineages. Finally, even with this extensive data set, the prophage diversity has not been fully grasped. This study shows how integrating the host population structure and clustering at the species level allows us to better appreciate phage diversity and its transmission dynamics.},
}
@article {pmid39315792,
year = {2024},
author = {Gu Liu, C and Thompson, BE and Chang, JD and Min, L and Maresso, AW},
title = {Construction and characterization of DNA libraries from cultured phages and environmental viromes.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0117124},
doi = {10.1128/aem.01171-24},
pmid = {39315792},
issn = {1098-5336},
abstract = {Despite many efforts to understand and leverage the functional potential of environmental viromes, most bacteriophage genes are largely uncharacterized. To explore novel biology from uncultivated microbes like phages, metagenomics has emerged as a powerful tool to directly mine new genes without the need to culture the diverse microbiota and the viruses within. When a pure computational approach cannot infer gene function, it may be necessary to create a DNA library from environmental genomic DNA, followed by the screening of that library for a particular function. However, these screens are often initiated without a metagenomic analysis of the completed DNA library being reported. Here, we describe the construction and characterization of DNA libraries from a single cultured phage (ΦT4), five cultured Escherichia coli phages, and three metagenomic viral sets built from freshwater, seawater, and wastewater samples. Through next-generation sequencing of five independent samplings of the libraries, we found a consistent number of recovered genes per replicate for each library, with many genes classifiable via the KEGG and Pharokka databases. By characterizing the size of the genes and inserts, we found that our libraries contain a median of one to two genes per contig with a median gene length of 303-381 bp for all libraries, reflective of the small genomes of viruses. The environmental libraries were genetically diverse compared to the single phage and multi-phage libraries. Additionally, we found reduced coverage of individual genomes when five phages were used as opposed to one. Taken together, this work provides a comprehensive analysis of the DNA libraries from phage genomes that can be used for metagenomic exploration and functional screens to infer and identify new biology.IMPORTANCEFunctional metagenomics is an approach that aims to characterize the putative biological function of genes in the microbial world. This includes an examination of the sequencing data collected from a pooled source of diverse microbes and inference of gene function by comparison to annotated and studied genes from public databases. At times, DNA libraries are made from these genes, and the library is screened for a specific function. Hits are validated using a combination of biological, computational, and structural analysis. Left unresolved is a detailed characterization of the library, both its diversity and content, for the purposes of imputing function entirely by computational means, a process that may yield findings that aid in designing useful screens to identify novel gene functions. In this study, we constructed libraries from cultured phages and uncultured viromes from the environment and characterized some important parameters, such as gene number, genes per contig, ratio of hypothetical to known proteins, total genomic coverage and recovery, and the effect of pooling genetic information from multiple sources, to provide a better understanding of the nature of these libraries. This work will aid the design and implementation of future screens of pooled DNA libraries to discover and isolate viral genes with novel biology across various biomes.},
}
@article {pmid39315779,
year = {2024},
author = {Rajeev, M and Jung, I and Kang, I and Cho, J-C},
title = {Genome-centric metagenomics provides insights into the core microbial community and functional profiles of biofloc aquaculture.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0078224},
doi = {10.1128/msystems.00782-24},
pmid = {39315779},
issn = {2379-5077},
abstract = {UNLABELLED: Bioflocs are microbial aggregates that play a pivotal role in shaping animal health, gut microbiota, and water quality in biofloc technology (BFT)-based aquaculture systems. Despite the worldwide application of BFT in aquaculture industries, our comprehension of the community composition and functional potential of the floc-associated microbiota (FAB community; ≥3 µm size fractions) remains rudimentary. Here, we utilized genome-centric metagenomic approach to investigate the FAB community in shrimp aquaculture systems, resulting in the reconstruction of 520 metagenome-assembled genomes (MAGs) spanning both bacterial and archaeal domains. Taxonomic analysis identified Pseudomonadota and Bacteroidota as core community members, with approximately 93% of recovered MAGs unclassified at the species level, indicating a large uncharacterized phylogenetic diversity hidden in the FAB community. Functional annotation of these MAGs unveiled their complex carbohydrate-degrading potential and involvement in carbon, nitrogen, and sulfur metabolisms. Specifically, genomic evidence supported ammonium assimilation, autotrophic nitrification, denitrification, dissimilatory nitrate reduction to ammonia, thiosulfate oxidation, and sulfide oxidation pathways, suggesting the FAB community's versatility for both aerobic and anaerobic metabolisms. Conversely, genes associated with heterotrophic nitrification, anaerobic ammonium oxidation, assimilatory nitrate reduction, and sulfate reduction were undetected. Members of Rhodobacteraceae emerged as the most abundant and metabolically versatile taxa in this intriguing community. Our MAGs compendium is expected to expand the available genome collection from such underexplored aquaculture environments. By elucidating the microbial community structure and metabolic capabilities, this study provides valuable insights into the key biogeochemical processes occurring in biofloc aquacultures and the major microbial contributors driving these processes.<br><br>IMPORTANCE: Biofloc technology has emerged as a sustainable aquaculture approach, utilizing microbial aggregates (bioflocs) to improve water quality and animal health. However, the specific microbial taxa within this intriguing community responsible for these benefits are largely unknown. Compounding this challenge, many bacterial taxa resist laboratory cultivation, hindering taxonomic and genomic analyses. To address these gaps, we employed metagenomic binning approach to recover over 500 microbial genomes from floc-associated microbiota of biofloc aquaculture systems operating in South Korea and China. Through taxonomic and genomic analyses, we deciphered the functional gene content of diverse microbial taxa, shedding light on their potential roles in key biogeochemical processes like nitrogen and sulfur metabolisms. Notably, our findings underscore the taxa-specific contributions of microbes in aquaculture environments, particularly in complex carbon degradation and the removal of toxic substances like ammonia, nitrate, and sulfide.},
}
@article {pmid39315152,
year = {2024},
author = {Zheng, B and Xu, J and Zhang, Y and Qin, J and Yuan, D and Fan, T and Wu, W and Chen, Y and Jiang, Y},
title = {MBCN: A novel reference database for Effcient Metagenomic analysis of human gut microbiome.},
journal = {Heliyon},
volume = {10},
number = {18},
pages = {e37422},
pmid = {39315152},
issn = {2405-8440},
abstract = {Metagenomic shotgun sequencing data can identify microbes and their proportions. But metagenomic shotgun data profiling results obtained from multiple projects using different reference databases are difficult to compare and apply meta-analysis. Our work aims to create a novel collection of human gut prokaryotic genomes, named Microbiome Collection Navigator (MBCN). 2379 human gut metagenomic samples are screened, and 16,785 metagenome-assembled genomes (MAGs) are assembled using a standardized pipeline. In addition, MAGs are combined with the representative genomes from public prokaryotic genomes collections to cluster, and pan-genomes for each cluster's genomes are constructed to build Kraken2 and Bracken databases. The databases built by MBCN are more comprehensive and accurate for profiling metagenomic reads comparing with other collections on simulated reads and virtual bio-projects. We profile 1082 human gut metagenomic samples with MBCN database and organize profiles and metadata on the web program. Meanwhile, using MBCN as a reference database, we also develop a unified, standardized, and systematic metagenomic analysis pipeline and platform, named MicrobiotaCN (http://www.microbiota.cn) and common statistical and visualization tools for microbiome research are integrated into the web program. Taken together, MBCN and MicrobiotaCN can be a valuable resource and a powerful tool that allows researchers to perform metagenomic analysis by a unified pipeline efficiently.},
}
@article {pmid39315098,
year = {2024},
author = {Li, K and Zhang, Y and Zhang, D and Chen, Q and Fang, X},
title = {Case report: Systemic multi-organ involvement in an adult-onset immunodeficiency patient infected with Talaromyces marneffei.},
journal = {Frontiers in immunology},
volume = {15},
number = {},
pages = {1430179},
pmid = {39315098},
issn = {1664-3224},
mesh = {Humans ; *Talaromyces ; Female ; Middle Aged ; *Mycoses/immunology/diagnosis/microbiology/drug therapy ; Antifungal Agents/therapeutic use ; Autoantibodies/immunology/blood ; High-Throughput Nucleotide Sequencing ; },
abstract = {Adult-onset immunodeficiency (AOID) mediated by anti-interferon-γ autoantibodies (AIGA) is a rare condition, particularly prevalent in Southeast Asia and southern China. We present a case study of a 62-year-old female with AOID who developed a severe pulmonary infection caused by Talaromyces marneffei (TM), leading to acute respiratory failure, generalized rash, multiple lymphadenopathies, bone destruction, and a mediastinal mass. Treatment included mechanical ventilation, antifungal medication, and corticosteroids, resulting in complete recovery and discharge. This case underscores the challenges of managing complex infections in AOID patients and highlights the importance of early diagnosis through metagenomic next-generation sequencing (mNGS) and appropriate intervention to improve clinical outcomes.},
}
@article {pmid39314983,
year = {2024},
author = {Golob, J and Rao, K and Berinstein, JA and Singh, P and Chey, WD and Owyang, C and Kamada, N and Higgins, PDR and Young, V and Bishu, S and Lee, AA},
title = {Why Symptoms Linger in Quiescent Crohn's Disease: Investigating the Impact of Sulfidogenic Microbes and Sulfur Metabolic Pathways.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.09.08.24313266},
pmid = {39314983},
abstract = {INTRODUCTION: Even in the absence of inflammation, persistent symptoms in patients with Crohn's disease (CD) are prevalent and worsen quality of life. We previously demonstrated enrichment in sulfidogenic microbes in quiescent Crohn's disease patients with (qCD+S) vs. without persistent GI symptoms (qCD-S). Thus, we hypothesized that sulfur metabolic pathways would be enriched in stool while differentially abundant microbes would be associated with important sulfur-metabolic pathways in qCD+S.<br><br>METHODS: We performed a multi-center observational study nested within SPARC IBD. Quiescent inflammation was defined by fecal calprotectin level <150 mcg/g. Persistent symptoms were defined by CD-PRO2. Active CD (aCD) and non-IBD diarrhea-predominant irritable bowel syndrome (IBS-D) were included as controls.<br><br>RESULTS: Thirty-nine patients with qCD+S, 274 qCD-S, 21 aCD, and 40 IBS-D underwent paired shotgun metagenomic sequencing and untargeted metabolomic profiling. The fecal metabolome in qCD+S was significantly different relative to qCD-S and IBS-D but not aCD. Patients with qCD+S were enriched in sulfur-containing amino acid pathways, including cysteine and methionine, as well as serine, glycine, and threonine. Glutathione and nicotinate/nicotinamide pathways were also enriched in qCD+S relative to qCD-S, suggestive of mitochondrial dysfunction, a downstream target of H 2 S signaling. Multi-omic integration demonstrated that enriched microbes in qCD+S were associated with important sulfur-metabolic pathways. Bacterial sulfur-metabolic genes, including CTH , isfD , sarD , and asrC , were dysregulated in qCD+S. Finally, sulfur metabolites with and without sulfidogenic microbes showed good accuracy in predicting presence of qCD+S.<br><br>DISCUSSION: Microbial-derived sulfur pathways and downstream mitochondrial function are perturbed in qCD+S, which implicate H 2 S signaling in the pathogenesis of this condition. Future studies will determine whether targeting H 2 S pathways results in improved quality of life in qCD+S.<br><br>KEY MESSAGES: What is Already Known Even in the absence of inflammation, persistent gastrointestinal symptoms are common in Crohn's disease.The microbiome is altered in quiescent Crohn's disease patients with persistent symptoms, but the functional significance of these changes is unknown. What is New Here Sulfur metabolites and sulfur metabolic pathways were enriched in stool in quiescent Crohn's disease patients with persistent symptoms.Multi-omic integration showed enriched microbes were associated with important sulfur metabolic pathways in quiescent Crohn's disease patients with persistent symptoms. How Can This Study Help Patient Care Strategies to decrease sulfidogenic microbes and associated sulfur metabolic pathways could represent a novel strategy to improve quality of life in quiescent Crohn's disease with persistent GI symptoms.},
}
@article {pmid39314554,
year = {2024},
author = {Bulata-Pop, I and Stirbu, I and Simionescu, B and Grama, A and Junie, LM},
title = {Clinical, Biological, and Radiological Findings and Management of Lower Respiratory Tract Infections in a Tertiary Hospital in Romania.},
journal = {Cureus},
volume = {16},
number = {8},
pages = {e67685},
pmid = {39314554},
issn = {2168-8184},
abstract = {Background Lower respiratory tract infections (LRTIs) remain a significant concern in pediatrics due to their substantial burden among childhood diseases. Romania has recently attained the status of a high-income country. Even though the mortality rate from respiratory diseases has significantly declined from 24.1 per 100,000 individuals in 2000 to 5.3 per 100,000 in 2022, the rate remains notably higher than the European average. Diagnosing LRTI is challenging due to its clinical similarity to noninfectious respiratory illness and frequent false-positive results or incidental findings on microbiologic tests. This often leads to antimicrobial overuse and adverse outcomes. Additionally, antibiotic resistance poses a significant global public health threat. Patients and method We conducted a retrospective analysis of pediatric LRTI cases at a tertiary pediatric center in Romania to evaluate diagnostic testing, imaging use, etiology identification, and treatment approaches. Children under 18, admitted to the Emergency Clinical Hospital for Children in Cluj-Napoca during an eight-month peak respiratory season, were included. Data from electronic medical records were analyzed for demographics, symptoms, physical exams, laboratory data, presence of fever, etiology, treatment, and outcomes. Results In total, 222 children were included in this study, with a median age of 29 months. Among the participants, 58% were male. The average hospital stay was 11 days. The total number of cases was almost equally split between bronchiolitis and pneumonia, with lobar pneumonia accounting for 12% of the included patients. We found two statistically significant correlations between the presence of fever, intercostal retracting, and the subtype of LRTI. An inflammatory response defined as an elevated leucocyte count and elevated C-reactive protein (CRP) was more likely to appear in pneumonia cases than bronchiolitis. From a therapeutic point of view, the prescription of hydrocortisone was statistically linked to bronchiolitis, but its use did not shorten hospitalization time. Conclusion Policy interventions and targeted treatments can reduce LRTI incidence and improve outcomes. Based on our correlations between specific clinical traits and subtypes of LRTIs, the use of assessment scores in children helps predict severe illness and the need for hospitalization. Promoting hygiene, social distancing, and addressing socioeconomic factors are crucial. Larger sample sizes and advanced diagnostics are needed to refine treatment strategies further. Early antibiotic use in children has long-term health implications, including a higher risk of respiratory-caused premature death in adulthood. This emphasizes the need for improved diagnostic processes and specific etiological identification, with metagenomics showing promise in this area.},
}
@article {pmid39314343,
year = {2024},
author = {Fuhrmeister, ER and Kim, S and Mairal, SA and McCormack, C and Chieng, B and Swarthout, JM and Paulos, AH and Njenga, SM and Pickering, AJ},
title = {Context-Seq: CRISPR-Cas9 Targeted Nanopore Sequencing for Transmission Dynamics of Antimicrobial Resistance.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.09.12.612745},
pmid = {39314343},
issn = {2692-8205},
abstract = {Antimicrobial resistance (AMR) aligns with a One Health framework in that resistant bacteria and antibiotic resistance genes (ARGs) can be transmitted between humans, animals, and the environment. However, there is a critical need to more precisely understand how and to what extent AMR is exchanged between animals and humans. Metagenomic sequencing has low detection for rare targets such as ARGs, while whole genome sequencing of isolates is burdensome and misses exchange between uncultured bacterial species. We developed a novel, targeted sequencing assay using CRISPR-Cas9 to selectively sequence ARGs and their genomic context with long-read sequencing. Using this method, termed Context-Seq, we investigated overlapping AMR elements containing the ARGs bla CTX-M and bla TEM between adults, children, poultry, and dogs in animal-owning households in Nairobi, Kenya. We identified 22 genetically distinct clusters (> 80%ID over ≥ 3000 bp) containing bla TEM and one cluster containing bla CTX-M that were shared within and between households. Half of the clusters were shared between humans and animals, while the other half were shared only between animals (poultry-poultry, dog-dog, and dog-poultry). We identified potentially pathogenic hosts of ARGs including Escherichia coli, Klebsiella pneumonia , and Haemophilus influenzae across sample types. Context-Seq complements conventional methods to obtain an additional view of bacterial and mammalian hosts in the proliferation of AMR.},
}
@article {pmid39314094,
year = {2024},
author = {Jiang, OY and Zhang, SY and Zhao, XD and Liu, ZT and Kappler, A and Xu, JM and Tang, XJ},
title = {Arsenic Reduces Methane Emissions from Paddy Soils: Insights from Continental Investigation and Laboratory Incubations.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c06809},
pmid = {39314094},
issn = {1520-5851},
abstract = {Arsenic (As) contamination and methane (CH4) emissions co-occur in rice paddies. However, how As impacts CH4 production, oxidation, and emission dynamics is unknown. Here, we investigated the abundances and activities of CH4-cycling microbes from 132 paddy soils with different As concentrations across continental China using metagenomics and the reverse transcription polymerase chain reaction. Our results revealed that As was a crucial factor affecting the abundance and distribution patterns of the mcrA gene, which is responsible for CH4 production and anaerobic CH4 oxidation. Laboratory incubation experiments showed that adding 30 mg kg[-1] arsenate increased [13]CO2 production by 10-fold, ultimately decreasing CH4 emissions by 68.5%. The inhibition of CH4 emissions by As was induced through three aspects: (1) the toxicity of As decreased the abundance and activity of the methanogens; (2) the adaptability and response of methanotrophs to As is beneficial for CH4 oxidation under As stress; and (3) the more robust arsenate reduction would anaerobically consume more CH4 in paddies. Additionally, significant positive correlations were observed between arsC and pmoA gene abundance in both the observational study and incubation experiment. These findings enhance our understanding of the mechanisms underlying the interactions between As and CH4 cycling in soils.},
}
@article {pmid39313845,
year = {2024},
author = {Maaskant, A and Voermans, B and Levin, E and de Goffau, MC and Plomp, N and Schuren, F and Remarque, EJ and Smits, A and Langermans, JAM and Bakker, J and Montijn, R},
title = {Microbiome signature suggestive of lactose-intolerance in rhesus macaques (Macaca mulatta) with intermittent chronic diarrhea.},
journal = {Animal microbiome},
volume = {6},
number = {1},
pages = {53},
pmid = {39313845},
issn = {2524-4671},
abstract = {BACKGROUND: Chronic diarrhea is a common cause of mortality and morbidity in captive rhesus macaques (Macaca mulatta). The exact etiology of chronic diarrhea in macaques remains unidentified. The occurrence of diarrhea is frequently linked to dysbiosis within the gut microbiome. Research into microbiome signatures correlated with diarrhea in macaques have predominantly been conducted with single sample collections. Our analysis was based on the metagenomic composition of longitudinally acquired fecal samples from rhesus macaques with chronic diarrhea and clinically healthy rhesus macaques that were obtained over the course of two years. We aimed to investigate potential relationships between the macaque gut microbiome, the presence of diarrhea and diet interventions with a selection of commercially available monkey diets.<br><br>RESULTS: The microbiome signature of macaques with intermittent chronic diarrhea showed a significant increase in lactate producing bacteria e.g. lactobacilli, and an increase in fermenters of lactate and succinate. Strikingly, two lactose free diets were associated with a lower incidence of diarrhea.<br><br>CONCLUSION: A lactose intolerance mechanism is suggested in these animals by the bloom of Lactobacillus in the presence of lactose resulting in an overproduction of intermediate fermentation products likely led to osmotically induced diarrhea. This study provides new insights into suspected microbiome-lactose intolerance relationship in rhesus macaques with intermittent chronic diarrhea. The integration of machine learning with metagenomic data analysis holds potential for developing targeted dietary interventions and therapeutic strategies and therefore ensuring a healthier and more resilient primate population.},
}
@article {pmid39282340,
year = {2024},
author = {Singh, H and Wiscovitch-Russo, R and Kuelbs, C and Espinoza, J and Appel, AE and Lyons, RJ and Vashee, S and Förtsch, HEA and Foster, JE and Ramdath, D and Hayes, VM and Nelson, KE and Gonzalez-Juarbe, N},
title = {Multiomic Insights into Human Health: Gut Microbiomes of Hunter-Gatherer, Agropastoral, and Western Urban Populations.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39282340},
issn = {2692-8205},
support = {R01 DK112381/DK/NIDDK NIH HHS/United States ; },
abstract = {Societies with exposure to preindustrial diets exhibit improved markers of health. Our study used a comprehensive multi-omic approach to reveal that the gut microbiome of the Ju/'hoansi hunter-gatherers, one of the most remote KhoeSan groups, exhibit a higher diversity and richness, with an abundance of microbial species lost in the western population. The Ju/'hoansi microbiome showed enhanced global transcription and enrichment of complex carbohydrate metabolic and energy generation pathways. The Ju/'hoansi also show high abundance of short-chain fatty acids that are associated with health and optimal immune function. In contrast, these pathways and their respective species were found in low abundance or completely absent in Western populations. Amino acid and fatty acid metabolism pathways were observed prevalent in the Western population, associated with biomarkers of chronic inflammation. Our study provides the first in-depth multi-omic characterization of the Ju/'hoansi microbiome, revealing uncharacterized species and functional pathways that are associated with health.},
}
@article {pmid38862509,
year = {2024},
author = {Overbey, EG and Ryon, K and Kim, J and Tierney, BT and Klotz, R and Ortiz, V and Mullane, S and Schmidt, JC and MacKay, M and Damle, N and Najjar, D and Matei, I and Patras, L and Garcia Medina, JS and Kleinman, AS and Wain Hirschberg, J and Proszynski, J and Narayanan, SA and Schmidt, CM and Afshin, EE and Innes, L and Saldarriaga, MM and Schmidt, MA and Granstein, RD and Shirah, B and Yu, M and Lyden, D and Mateus, J and Mason, CE},
title = {Collection of biospecimens from the inspiration4 mission establishes the standards for the space omics and medical atlas (SOMA).},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {4964},
pmid = {38862509},
issn = {2041-1723},
support = {R01 ES032638/ES/NIEHS NIH HHS/United States ; R01 MH117406/MH/NIMH NIH HHS/United States ; },
mesh = {*Specimen Handling/standards ; Humans ; *Space Flight ; *Biological Specimen Banks/standards ; Exobiology ; *Preservation, Biological/standards ; Metagenomics/standards ; },
abstract = {The SpaceX Inspiration4 mission provided a unique opportunity to study the impact of spaceflight on the human body. Biospecimen samples were collected from four crew members longitudinally before (Launch: L-92, L-44, L-3 days), during (Flight Day: FD1, FD2, FD3), and after (Return: R + 1, R + 45, R + 82, R + 194 days) spaceflight, spanning a total of 289 days across 2021-2022. The collection process included venous whole blood, capillary dried blood spot cards, saliva, urine, stool, body swabs, capsule swabs, SpaceX Dragon capsule HEPA filter, and skin biopsies. Venous whole blood was further processed to obtain aliquots of serum, plasma, extracellular vesicles and particles, and peripheral blood mononuclear cells. In total, 2,911 sample aliquots were shipped to our central lab at Weill Cornell Medicine for downstream assays and biobanking. This paper provides an overview of the extensive biospecimen collection and highlights their processing procedures and long-term biobanking techniques, facilitating future molecular tests and evaluations.As such, this study details a robust framework for obtaining and preserving high-quality human, microbial, and environmental samples for aerospace medicine in the Space Omics and Medical Atlas (SOMA) initiative, which can aid future human spaceflight and space biology experiments.},
}
@article {pmid39313703,
year = {2024},
author = {Talib, N and Mohamad, NE and Ho, CL and Masarudin, MJ and Alitheen, NB},
title = {Modulatory Effects of Isolated Lactobacillus paracasei from Malaysian Water Kefir Grains on the Intestinal Barrier and Gut Microbiota in Diabetic Mice.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {39313703},
issn = {1867-1314},
support = {FRGS/1/2017/SKK10/UPM/02/4 and FRGS-MRSA/1/2018/SKK10/UPM/02/1//Ministry of Education, Government of Malaysia./ ; },
abstract = {Type 2 diabetes (T2DM) is one of the four major types of non-communicable diseases that have become a global health concern. Water kefir is a product of a brown sugar solution fermented with kefir grains which comprises around 30 microbial species in its grains. Water kefir possesses a wide range of health benefits, including anti-hyperlipidemic effects, and reduces hypertension and blood glucose levels in animal models. Reportedly, consuming water kefir containing probiotics may enhance the intestinal barrier and positively influence the composition of the intestinal microflora. The present study aimed to evaluate the regulatory effects of Lactobacillus paracasei isolated from Malaysian water kefir grains (MWKG) on the alterations of intestinal barrier and gut microbiota in diabetic mice via histopathological analysis of the distal colon and 16S rRNA gene sequencing on fecal microbiome. Results indicated that the administration of isolated Lactobacillus paracasei from MWKG to diabetic mice ameliorated the dominant probiotic phyla in the gut microbiota. Results showed that lower dose (LD) and high dose (HD) treatments of the isolated Lactobacillus paracasei could significantly reduce inflammatory cell infiltration in the distal colon of diabetic mice. The treatments revealed a significant decrease in the relative abundance of Firmicutes in the gut, 0.27 ± 0.06% for LD and 0.34 ± 0.04% for HD, compared to untreated (UN) diabetic mice, 0.40 ± 0.02%. These results suggest that L. paracasei isolated from MWKG could serve as a potential dietary supplement against intestinal inflammation and modify gut microbiota composition in patients with T2DM.},
}
@article {pmid39313592,
year = {2024},
author = {Hemapriya, M and Nataraja, KN and Suryanarayanan, TS and Uma Shaanker, R},
title = {Comparative Metagenomic Analysis of Seed Endobiome of Domesticated and Wild Finger Millet Species (Eleusine spp.): Unveiling Microbial Diversity and Composition.},
journal = {Current microbiology},
volume = {81},
number = {11},
pages = {373},
pmid = {39313592},
issn = {1432-0991},
abstract = {Domestication, which involves selective breeding, modern agricultural practices, and specific growing conditions, can influence the microbial and endophytic communities in crop plants. In this study, we examined the microbial diversity and community composition in the seeds of wild and domesticated finger millet species. We employed a metagenomic approach to investigate the seed microbial diversity and community composition of wild (Eleusine africana) and domesticated finger millet species (Eleusine coracana (L.) Gaertn) grown in the same habitat. While our findings indicated no significant change in seed endobiome diversity due to domestication, there were differences in microbial community composition between wild and domesticated species. Seeds of domesticated species had higher relative abundance of certain bacterial genera including Helicobacter, Akkermansia, Streptococcus, Bacteroides, and Pseudomonas, whereas seeds of wild species had higher relative abundance of unclassified Streptophyta. The seed-associated microbiota also varied among domesticated finger millet accessions. Co-occurrence network analysis revealed a strong relationship between bacteria and fungi in domesticated compared to wild species. We discuss the results obtained in the larger context of the importance of seed endobiome and how domestication processes in crop plants may have impacted the seed endobiome diversity, composition, and function compared to their wild counterparts.},
}
@article {pmid39313228,
year = {2024},
author = {Kirtipal, N and Seo, Y and Son, J and Lee, S},
title = {Systems Biology of Human Microbiome for the Prediction of Personal Glycaemic Response.},
journal = {Diabetes &amp; metabolism journal},
volume = {48},
number = {5},
pages = {821-836},
doi = {10.4093/dmj.2024.0382},
pmid = {39313228},
issn = {2233-6087},
support = {//Ministry of Science ICT/ ; 2021R1C1C1006336//National Research Foundation of Korea/ ; 2021M3A9G8022959//National Research Foundation of Korea/ ; RS-2024-00419699//National Research Foundation of Korea/ ; //Korea Health Industry Development Institute/ ; HR22C141105//Ministry of Health and Welfare/ ; 2024-ER2108-00//Korea National Institute of Health/ ; 2024-ER0608-00//Korea National Institute of Health/ ; //GIST Research Institute/ ; },
abstract = {The human gut microbiota is increasingly recognized as a pivotal factor in diabetes management, playing a significant role in the body's response to treatment. However, it is important to understand that long-term usage of medicines like metformin and other diabetic treatments can result in problems, gastrointestinal discomfort, and dysbiosis of the gut flora. Advanced sequencing technologies have improved our understanding of the gut microbiome's role in diabetes, uncovering complex interactions between microbial composition and metabolic health. We explore how the gut microbiota affects glucose metabolism and insulin sensitivity by examining a variety of -omics data, including genomics, transcriptomics, epigenomics, proteomics, metabolomics, and metagenomics. Machine learning algorithms and genome-scale modeling are now being applied to find microbiological biomarkers associated with diabetes risk, predicted disease progression, and guide customized therapy. This study holds promise for specialized diabetic therapy. Despite significant advances, some concerns remain unanswered, including understanding the complex relationship between diabetes etiology and gut microbiota, as well as developing user-friendly technological innovations. This mini-review explores the relationship between multiomics, precision medicine, and machine learning to improve our understanding of the gut microbiome's function in diabetes. In the era of precision medicine, the ultimate goal is to improve patient outcomes through personalized treatments.},
}
@article {pmid39313124,
year = {2024},
author = {Wu, C and Hang, S and Li, F and Wu, Y and Yi, S and Liu, X and Chen, M and Ge, F and Tian, J and Zhang, M and Zhang, D},
title = {DNA-stable isotope probing and metagenomics reveal Fe(II) oxidation by core microflora in microoxic rhizospheric habitats to mitigate the accumulation of cadmium and phenanthrene in rice.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {125012},
doi = {10.1016/j.envpol.2024.125012},
pmid = {39313124},
issn = {1873-6424},
abstract = {Rice rhizosphere soil-porewater microdomains exist within an iron (Fe)-rich microoxic habitat during paddy soil flooding. However, the response mechanisms of core microflora in this habitat to Fe(II)-oxidation-mediated cadmium (Cd) and phenanthrene (Phen) remain unclear. Using gel-stabilized gradient systems to replicate the microoxic conditions in the rice rhizosphere porewater, we found that microaerophilic rhizobacteria drove Fe(II) oxidation to yield iron oxides, thereby reducing the Cd and Phen contents in the rhizosphere porewater and rice (Cd and Phen decreased by 15.9%-78.0% and 10.1%-37.4%, respectively). However, co-exposure to Cd and Phen resulted in a greater reduction in the Cd uptake and a greater increase in the Phen uptake in rice as compared to those in the Cd or Phen treatments, possibly attributing to the cation-π interactions between Cd and Phen, as well as competition between the adsorption sites on the roots. The elevation of Cd-tolerant genes and Phen-degradation genes in biogenic cell-mineral aggregates unveiled the survival strategies of rhizobacteria with respect to Cd and Phen in the microoxic habitat. Potential Cd-tolerant rhizobacteria (e.g., Pandoraea and Comamonas) and Phen-degradation rhizobacteria (e.g., Pseudoxanthobacter) were identified through the DNA-SIP and 16S rRNA gene amplicon sequencing. Metagenomic analysis further confirmed that these core microbes harbor Cd-tolerant, Phen-degradation, and Fe(II) oxidation genes, supporting their metabolic potential for Cd and/or Phen in the microoxic habitat of the rice rhizosphere. These findings suggest the potential mechanism and ecological significance of core rhizospheric microbial-driven Fe(II) oxidation in mitigating the bioavailability of Cd and Phen in paddy soil during flooding.},
}
@article {pmid39312587,
year = {2024},
author = {de Campos, GM and Santos, HO and Lima, ARJ and Leite, AB and Ribeiro, G and Todão Bernardino, JS and do Nascimento, JPM and Souza, JVC and de Lima, LPO and Lima, MBZ and de Araújo, MA and Giovanetti, M and Kallas, EG and Sampaio, SC and Elias, MC and Slavov, SN},
title = {Unveiling viral pathogens in acute respiratory disease: Insights from viral metagenomics in patients from the State of Alagoas, Brazil.},
journal = {PLoS neglected tropical diseases},
volume = {18},
number = {9},
pages = {e0012536},
doi = {10.1371/journal.pntd.0012536},
pmid = {39312587},
issn = {1935-2735},
abstract = {BACKGROUND: Respiratory illness affects individuals across all age demographics on a global scale, often precipitated by viral infections. The symptomatic manifestations of these diseases bear clinical resemblance, complicating the accurate determination of their etiological origins. Furthermore, the diagnostic panels for respiratory pathogens used within local medical practices, may not encompass the full spectrum of viral agents responsible for such ailments. Consequently, a significant number of clinically important viral pathogens may remain undetected.<br><br>METHODS AND FINDINGS: In the light of this, we conducted a metagenomic examination of 66 nasopharyngeal swab specimens, obtained from patients presenting with acute respiratory conditions yet tested negative by the standard diagnostic panels available locally. These specimens were obtained from the Public Health Laboratory, Maceio, State of Alagoas. Our findings indicate a predominant diagnostic escape of rhinoviruses and notably enterovirus D68. Moreover, our study identified a substantial quantity of sequence reads attributed to human respirovirus 3 (human parainfluenza 3) along with various herpresviruses including human herpesvirus-1, Epstein-Barr virus (Human herpesvirus-4), Human herpesviruses 6 and 7 and human parvovirus B19 (B19V). Notably, the metagenomic analysis uncovered a widespread presence of the emerging human vientovirus FB in most of sample pools, though its clinical importance remains to be elucidated.<br><br>CONCLUSIONS: The obtained results in this study underscore the invaluable role of viral metagenomics in the identification of underrecognized viruses bearing clinical relevance. Furthermore, it offers insights into the dissemination of these pathogens within the studied area, thereby informing public health strategies aimed at enhancing diagnostic accuracy and improving patient care.},
}
@article {pmid39312489,
year = {2024},
author = {Zhang, L and Meng, L and Fang, Y and Ogata, H and Okazaki, Y},
title = {Spatiotemporal dynamics of giant viruses within a deep freshwater lake reveal a distinct dark-water community.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae182},
pmid = {39312489},
issn = {1751-7370},
abstract = {Giant viruses significantly regulate the ecological dynamics of diverse ecosystems. Although metagenomics has expanded our understanding of their diversity and ecological roles played in marine environments, little is known about giant viruses of freshwater ecosystems. Most previous studies have employed short-read sequencing and therefore resulted in fragmented genomes, hampering accurate assessment of genetic diversity. We sought to bridge this knowledge gap and overcome previous technical limitations. We subjected spatiotemporal (2 depths × 12 months) samples from Lake Biwa to metagenome-assembled genome reconstruction enhanced by long-read metagenomics. This yielded 293 giant virus metagenome-assembled genomes. Of these, 285 included previously unknown species in five orders of nucleocytoviruses and the first representatives of freshwater mirusviruses, which exhibited marked divergence from marine-derived lineages. The good performance of our long-read metagenomic assembly was demonstrated by the detection of 42 (14.3%) genomes composed of single contigs with completeness values >90%. Giant viruses were partitioned across water depths, with most species specific to either the sunlit epilimnion or the dark hypolimnion. Epilimnion-specific members tended to be transient and exhibit short and intense abundance peaks, in line with the fact that they regulate the surface algal blooms. During the spring bloom, mirusviruses and members of three nucleocytovirus families were among the most abundant viruses. In contrast, hypolimnion-specific ones including a mirusvirus genome were typically more persistent in the hypolimnion throughout the water-stratified period, suggesting that they infect hosts specific to the hypolimnion and play previously unexplored ecological roles in dark water microbial ecosystems.},
}
@article {pmid39311770,
year = {2024},
author = {Zhou, B and Wang, C and Putzel, G and Hu, J and Liu, M and Wu, F and Chen, Y and Pironti, A and Li, H},
title = {An integrated strain-level analytic pipeline utilizing longitudinal metagenomic data.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0143124},
doi = {10.1128/spectrum.01431-24},
pmid = {39311770},
issn = {2165-0497},
abstract = {UNLABELLED: With the development of sequencing technology and analytic tools, studying within-species variations enhances the understanding of microbial biological processes. Nevertheless, most existing methods designed for strain-level analysis lack the capability to concurrently assess both strain proportions and genome-wide single nucleotide variants (SNVs) across longitudinal metagenomic samples. In this study, we introduce LongStrain, an integrated pipeline for the analysis of large-scale metagenomic data from individuals with longitudinal or repeated samples. In LongStrain, we first utilize two efficient tools, Kraken2 and Bowtie2, for the taxonomic classification and alignment of sequencing reads, respectively. Subsequently, we propose to jointly model strain proportions and shared haplotypes across samples within individuals. This approach specifically targets tracking a primary strain and a secondary strain for each subject, providing their respective proportions and SNVs as output. With extensive simulation studies of a microbial community and single species, our results demonstrate that LongStrain is superior to two genotyping methods and two deconvolution methods across a majority of scenarios. Furthermore, we illustrate the potential applications of LongStrain in the real data analysis of The Environmental Determinants of Diabetes in the Young study and a gastric intestinal metaplasia microbiome study. In summary, the proposed analytic pipeline demonstrates marked statistical efficiency over the same type of methods and has great potential in understanding the genomic variants and dynamic changes at strain level. LongStrain and its tutorial are freely available online at https://github.com/BoyanZhou/LongStrain.<br><br>IMPORTANCE: The advancement in DNA-sequencing technology has enabled the high-resolution identification of microorganisms in microbial communities. Since different microbial strains within species may contain extreme phenotypic variability (e.g., nutrition metabolism, antibiotic resistance, and pathogen virulence), investigating within-species variations holds great scientific promise in understanding the underlying mechanism of microbial biological processes. To fully utilize the shared genomic variants across longitudinal metagenomics samples collected in microbiome studies, we develop an integrated analytic pipeline (LongStrain) for longitudinal metagenomics data. It concurrently leverages the information on proportions of mapped reads for individual strains and genome-wide SNVs to enhance the efficiency and accuracy of strain identification. Our method helps to understand strains' dynamic changes and their association with genome-wide variants. Given the fast-growing longitudinal studies of microbial communities, LongStrain which streamlines analyses of large-scale raw sequencing data should be of great value in microbiome research communities.},
}
@article {pmid39311668,
year = {2024},
author = {Rigkos, K and Filis, G and Antonopoulou, I and de Oliveira Maciel, A and Saridis, P and Zarafeta, D and Skretas, G},
title = {Biomimetic CO2 Capture Unlocked through Enzyme Mining: Discovery of a Highly Thermo- and Alkali-Stable Carbonic Anhydrase.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c04291},
pmid = {39311668},
issn = {1520-5851},
abstract = {Taking immediate action to combat the urgent threat of CO2-driven global warming is crucial for ensuring a habitable planet. Decarbonizing the industrial sector requires implementing sustainable carbon-capture technologies, such as biomimetic hot potassium carbonate capture (BioHPC). BioHPC is superior to traditional amine-based strategies due to its eco-friendly nature. This innovative technology relies on robust carbonic anhydrases (CAs), enzymes that accelerate CO2 hydration and endure harsh industrial conditions like high temperature and alkalinity. Thus, the discovery of highly stable CAs is crucial for the BioHPC technology advancement. Through high-throughput bioinformatics analysis, we identified a highly thermo- and alkali-stable CA, termed CA-KR1, originating from a metagenomic sample collected at a hot spring in Kirishima, Japan. CA-KR1 demonstrates remarkable stability at high temperatures and pH, with a half-life of 24 h at 80 °C and retains activity and solubility even after 30 d in a 20% (w/v) K2CO3/pH 11.5 solution─a standard medium for HPC. In pressurized batch reactions, CA-KR1 enhanced CO2 absorption by >90% at 90 °C, 20% K2CO3, and 7 bar. To our knowledge, CA-KR1 constitutes the most resilient CA biocatalyst for efficient CO2 capture under HPC-relevant conditions, reported to date. CA-KR1 integration into industrial settings holds great promise in promoting efficient BioHPC, a potentially game-changing development for enhancing carbon-capture capacity toward industrial decarbonization.},
}
@article {pmid39310785,
year = {2024},
author = {Li, Z and Tan, L and Zhang, J and Long, Q and Chen, Z and Xiang, Z and Wu, W and Guo, Z and Liu, H and Hu, B and Yang, B and Hu, M},
title = {Diagnostic performance of metagenomic sequencing in patients with suspected infection: a large-scale retrospective study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1463081},
pmid = {39310785},
issn = {2235-2988},
mesh = {Humans ; Retrospective Studies ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; Female ; Male ; Middle Aged ; Adult ; *Sensitivity and Specificity ; Communicable Diseases/diagnosis/microbiology ; Aged ; Young Adult ; Adolescent ; Child ; Molecular Diagnostic Techniques/methods ; Respiratory Tract Infections/diagnosis/microbiology ; Child, Preschool ; },
abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) has been widely reported to identify pathogens in infectious diseases (IDs). In this work, we intended to investigate the diagnostic value and clinical acceptance of paired-samples mNGS as compared to the culture method.<br><br>METHODS: A total of 361 patients with suspected infection were retrospectively included. With reference to the clinical diagnosis, we compared the diagnostic performance and clinical acceptance in pathogen detection between mNGS and culture tests. Moreover, the pathogen concordance of paired blood and respiratory tract (RT) samples in mNGS assay was investigated.<br><br>RESULTS: Among 511 samples, 62.04% were shown to be pathogen positive by mNGS, and that for clinical diagnosis was 51.86% (265/511). When compared to culture assay (n = 428), mNGS had a significantly higher positivity rate (51.87% vs. 33.18%). With reference to the clinical diagnosis, the sensitivity of mNGS outperformed that of culture (89.08% vs. 56.72%). Importantly, mNGS exhibited a clinically accepted rate significantly superior to that of culture. In addition, the mNGS result from 53 paired blood and RT samples showed that most pairs were pathogen positive by both blood and RT, with pathogens largely being partially matched.<br><br>CONCLUSION: Through this large-scale study, we further illustrated that mNGS had a clinically accepted rate and sensitivity superior to those of the traditional culture method in diagnosing infections. Moreover, blood and paired RT samples mostly shared partial-matched positive pathogens, especially for pathogens with abundant read numbers in RT, indicating that both blood and RT mNGS can aid the identification of pathogens for respiratory system infection.},
}
@article {pmid39309265,
year = {2024},
author = {Zeng, T and Lin, C and Deng, Y and Zhu, W},
title = {Effect of BF839 + earthworm protein supplement on motor and some non-motor symptoms of Parkinson's disease: a randomized clinical trial.},
journal = {Frontiers in neurology},
volume = {15},
number = {},
pages = {1371791},
pmid = {39309265},
issn = {1664-2295},
abstract = {INTRODUCTION: Some studies have found that probiotics have the potential to treat PD, and earthworm protein is a traditional Chinese medicine used for the treatment of PD. The purpose of this study was to evaluate the safety and efficacy of Bacteroides fragilis 839 (BF839) + earthworm protein supplement as an adjunctive therapy for PD and to observe changes in the gut microbiota.<br><br>METHODS: Forty-six patients with PD were recruited for a 12-week 1:1 randomized, double-blind, placebo-controlled clinical trial to evaluate changes in motor and some non-motor symptom scores and detect metagenomic changes in the gut microbiota.<br><br>RESULTS: From baseline to 12&#x2009;weeks, compared with placebo, the trial group showed significant reductions in the United Parkinson's Disease Rate Scale (UPDRS) total score (-7.74&#x2009;&#xb1;&#x2009;5.92 vs. -1.83&#x2009;&#xb1;&#x2009;4.14, p&#x2009;<&#x2009;0.001), UPDRS part I (-0.72&#x2009;&#xb1;&#x2009;0.81 vs. -0.20&#x2009;&#xb1;&#x2009;0.72, p&#x2009;=&#x2009;0.026), UPDRS part II (-2.50&#x2009;&#xb1;&#x2009;2.24 vs. -0.22&#x2009;&#xb1;&#x2009;1.98, p&#x2009;=&#x2009;0.001), UPDRS part III (-3.43&#x2009;&#xb1;&#x2009;3.42 vs. -1.33&#x2009;&#xb1;&#x2009;2.65, p&#x2009;=&#x2009;0.024), and UPDRS part IV (-1.13&#x2009;&#xb1;&#x2009;1.19 vs. -0.15&#x2009;&#xb1;&#x2009;0.57, p&#x2009;=&#x2009;0.001). Significant reductions in the Hamilton Depression Scale-24 score (-3.91&#x2009;&#xb1;&#x2009;3.99 vs. +1.15&#x2009;&#xb1;&#x2009;3.42, p&#x2009;<&#x2009;0.001), Self-Rating Anxiety Scale scores (-7.04&#x2009;&#xb1;&#x2009;5.71 vs. -1.23&#x2009;&#xb1;&#x2009;2.34, p&#x2009;<&#x2009;0.001), and Constipation scoring system scores (-8.59&#x2009;&#xb1;&#x2009;4.75 vs. 0.27&#x2009;&#xb1;&#x2009;1.24, p&#x2009;<&#x2009;0.001), were also noted. In the trial group, one patient experienced mild eczema and one suffered low blood pressure, which could not be conclusively attributed to supplementation. Compared to the placebo group, the trial group showed a marked increase in Enterococcus faecium and a decrease in Klebsiella.<br><br>CONCLUSION: This study is the first to report that probiotics plus earthworm protein can remarkably improve the motor and some non-motor symptoms of PD without serious adverse effects. However, further clinical trials and exploration of the underlying mechanisms are required.<br><br>CLINICAL TRIAL REGISTRATION: Clinical trial registry http://www.chictr.org.cn/, Identification No: ChiCTR2000035122.},
}
@article {pmid39308956,
year = {2024},
author = {Junier, P and Cailleau, G and Fatton, M and Udriet, P and Hashmi, I and Bregnard, D and Corona-Ramirez, A and Francesco, ED and Kuhn, T and Mangia, N and Zhioua, S and Hunkeler, D and Bindschedler, S and Sieber, S and Gonzalez, D},
title = {A cohesive Microcoleus strain cluster causes benthic cyanotoxic blooms in rivers worldwide.},
journal = {Water research X},
volume = {24},
number = {},
pages = {100252},
pmid = {39308956},
issn = {2589-9147},
abstract = {Over the last two decades, proliferations of benthic cyanobacteria producing derivatives of anatoxin-a have been reported in rivers worldwide. Here, we follow up on such a toxigenic event happening in the Areuse river in Switzerland and investigate the diversity and genomics of major bloom-forming riverine benthic cyanobacteria. We show, using 16S rRNA-based community profiling, that benthic communities are dominated by Oscillatoriales. We correlate the detection of one Microcoleus sequence variant matching the Microcoleus anatoxicus species with the presence of anatoxin-a derivatives and use long-read metagenomics to assemble complete circular genomes of the strain. The main dihydro-anatoxin-a-producing strain in the Areuse is distinct from strains isolated in New Zealand, the USA, and Canada, but forms a monophyletic strain cluster with them with average nucleotide identity values close to the species threshold. Compared to the rest of the Microcoleus genus, the toxin-producing strains encode a 15 % smaller genome, lacking genes for the synthesis of some essential vitamins. Toxigenic mats harbor a distinct microbiome dominated by proteobacteria and bacteroidetes, which may support cyanobacterial growth by providing them with essential nutrients. We recommend that strains closely related to M. anatoxicus be monitored internationally in order to help predict and mitigate similar cyanotoxic events.},
}
@article {pmid39308639,
year = {2024},
author = {Prosperi, M and Marini, S and Boucher, C},
title = {An average-case efficient two-stage algorithm for enumerating all longest common substrings of minimum length k between genome pairs.},
journal = {Proceedings. IEEE International Conference on Healthcare Informatics},
volume = {2024},
number = {},
pages = {93-102},
pmid = {39308639},
issn = {2575-2626},
abstract = {A problem extension of the longest common substring (LCS) between two texts is the enumeration of all LCSs given a minimum length k (ALCS- k), along with their positions in each text. In bioinformatics, an efficient solution to the ALCS- k for very long texts -genomes or metagenomes- can provide useful insights to discover genetic signatures responsible for biological mechanisms. The ALCS- k problem has two additional requirements compared to the LCS problem: one is the minimum length k , and the other is that all common strings longer than k must be reported. We present an efficient, two-stage ALCS- k algorithm exploiting the spectrum of text substrings of length k (k -mers). Our approach yields a worst-case time complexity loglinear in the number of k -mers for the first stage, and an average-case loglinear in the number of common k -mers for the second stage (several orders of magnitudes smaller than the total k -mer spectrum). The space complexity is linear in the first phase (disk-based), and on average linear in the second phase (disk- and memory-based). Tests performed on genomes for different organisms (including viruses, bacteria and animal chromosomes) show that run times are consistent with our theoretical estimates; further, comparisons with MUMmer4 show an asymptotic advantage with divergent genomes.},
}
@article {pmid39308020,
year = {2024},
author = {Kong, X and Dong, Z and Hu, W and Mi, J and Xiao, J and Wang, Y and Chen, W and Pei, Z and Hao, Z and Liang, C and Wang, Q and Wang, Z},
title = {The role of gut microbiota involved in prostate microenvironment and symptoms improvement in chronic prostatitis/chronic pelvic pain syndrome patients treated with low-intensity extracorporeal shock wave.},
journal = {The Prostate},
volume = {},
number = {},
pages = {},
doi = {10.1002/pros.24794},
pmid = {39308020},
issn = {1097-0045},
support = {2020QN-15//"Cuiying Science and Technology Innovation" Program/ ; CYXZ2022-40, CYXZ2022-23//Of the Second Hospital of Lanzhou University, The "Cuiying Scholars" Program of the Second Hospital of Lanzhou University/ ; 2021B-042//The Innovation Fund Project of the Gansu Provincial Education Department/ ; PRO133011//National Natural Science Foundation of China/ ; lzujbky-2021-kb29//The Fundamental Research Funds for the Central Universities of Lanzhou University/ ; //and Natural Science Foundation of G/ ; },
abstract = {BACKGROUND: Low-intensity extracorporeal shockwave therapy (Li-ESWT) is emerging as a promising and safe treatment for Chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS). In this study, we aimed to investigate the role of the gut microbiota involved in the prostate microenvironment and symptom improvement during the Li-ESWT for CP/CPPS patients.<br><br>METHODS: CP/CPPS patients not taking antibiotics or other treatments were included. NIH-Chronic Prostatitis Symptom Index (NIH-CPSI), International Prostate Symptom Score (IPSS), and International Index of Erectile Function (IIEF-5) were used to evaluate the effectiveness of Li-ESWT at the end of treatment. Visual analogue scale/score was used to evaluate the pain during procedure. Stool and semen samples were collected before and after Li-ESWT. Shotgun metagenomics analyzed gut microbiota, while ELISA and other diagnostic kits detected biochemical changes in seminal plasma.<br><br>RESULT: Of the 60 enrolled patients, 52 completed treatment. Li-ESWT response rate was 78.8% (41/52) at end of treatment. Among responders, the subitems of the NIH-CPSI; IPSS; and IIEF-5 scores improved significantly, and the seminal plasma analysis showed decreased TNF-a and MDA levels and increased SOD and Zn[2+] levels posttreatment. Gut microbiome analysis indicated that posttreatment, both &#x3b1; and &#x3b2; diversity increased, and the abundance of certain specific species significantly increased. Fifty-eight pathways significantly enriched posttreatment, notably in branched-chain amino acid synthesis and butyrate synthesis. The abundance of several specific species was found to be significantly higher in non-responders than responders. Among responders, at the species level, some bacteria associated with NIH-CPSI and its subscales, IPSS, IIEF-5, and prostate microenvironment markers (TNF-a, MDA, Zn[2+], and SOD) were identified.<br><br>CONCLUSIONS: Our study demonstrates for the first time that Li-ESWT improves the prostate microenvironment and gut microbiota in CP/CPPS patients. Treatment nonresponse may be associated with a high abundance of specific pathogens before treatment. The gut microbiota could have a significant impact on Li-ESWT response and the prostate microenvironment.},
}
@article {pmid39193769,
year = {2024},
author = {Smith, TA and Srikanth, K and Huson, HJ},
title = {Comparative Population Genomics of Arctic Sled Dogs Reveals a Deep and Complex History.},
journal = {Genome biology and evolution},
volume = {16},
number = {9},
pages = {},
pmid = {39193769},
issn = {1759-6653},
support = {2021-22//University of Maryland, Baltimore County/ ; //Neogen Genomics/ ; //Siberian Husky Club of America/ ; },
mesh = {*Dogs/classification/genetics ; *Metagenomics ; Arctic Regions ; Phylogeny ; },
abstract = {Recent evidence demonstrates genomic and morphological continuity in the Arctic ancestral lineage of dogs. Here, we use the Siberian Husky to investigate the genomic legacy of the northeast Eurasian Arctic lineage and model the deep population history using genome-wide single nucleotide polymorphisms. Utilizing ancient dog-calibrated molecular clocks, we found that at least two distinct lineages of Arctic dogs existed in ancient Eurasia at the end of the Pleistocene. This pushes back the origin of sled dogs in the northeast Siberian Arctic with humans likely intentionally selecting dogs to perform different functions and keeping breeding populations that overlap in time and space relatively reproductively isolated. In modern Siberian Huskies, we found significant population structure based on how they are used by humans, recent European breed introgression in about half of the dogs that participate in races, moderate levels of inbreeding, and fewer potentially harmful variants in populations under strong selection for form and function (show, sled show, and racing populations of Siberian Huskies). As the struggle to preserve unique evolutionary lineages while maintaining genetic health intensifies across pedigreed dogs, understanding the genomic history to guide policies and best practices for breed management is crucial to sustain these ancient lineages and their unique evolutionary identity.},
}
@article {pmid39307865,
year = {2024},
author = {Gundogdu, A and Nalbantoglu, OU and Karis, G and Sarikaya, I and Erdogan, MN and Hora, M and Aslan, H},
title = {Comparing microbial communities in mucilage and seawater samples: Metagenomic insights into mucilage formation in the Marmara Sea.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
doi = {10.1007/s11356-024-34968-2},
pmid = {39307865},
issn = {1614-7499},
support = {121G128//The Scientific and Technological Research Council of Turkey (TUBITAK)/ ; },
abstract = {Marine environments are subject to various naturally occurring phenomena, including marine snow and mucilage. In 2021, the rapid emergence of mucilage in the Marmara Sea raised concerns about its environmental impact. This study investigates the microbial communities in mucilage and seawater samples from the Marmara Sea using metagenomic-scale comparative analyses. The results indicate significant differences in microbial composition and diversity, with mucilage samples showing higher levels of polysaccharide biosynthesis-related enzymes. Over 50% of reads in mucilage samples remained unclassified (dark matter), highlighting unknown microbial taxa. Clean seawater was characterized by a higher presence of Euryarchaeota, Proteobacteria, and Rhodothermaeota, while Chlamydiae and Fusobacteria were dominant in mucilage. The study underscores the necessity for comprehensive metagenomic analyses to understand microbial roles in mucilage formation and persistence. Early detection of microbial shifts could serve as a warning system for mucilage outbreaks, aiding in the development of management strategies.},
}
@article {pmid39307589,
year = {2024},
author = {Koike, Y and Kuwatsuka, S and Motooka, D and Murota, H},
title = {Dysbiosis of the human skin mycobiome in patients receiving systemic IL-23 inhibitors.},
journal = {Allergology international : official journal of the Japanese Society of Allergology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.alit.2024.06.003},
pmid = {39307589},
issn = {1440-1592},
abstract = {BACKGROUND: Systemic inhibition of pro-inflammatory cytokines affects the skin microbiome; however, the impact of systemic anti-inflammatory therapy on the skin fungal microbiome is poorly understood. To examine the effects of cytokine inhibition on the fungal community on human skin and oral mucosa, we analyzed the composition of the skin mycobiome before and after IL-23 inhibition.<br><br>METHODS: The study enrolled 15 psoriasis patients. Swab samples were collected from the psoriasis-free skin of antecubital fossa, post-auricular, and the tongue surface before and after 16 weeks of treatment with anti-IL-23 antibodies. Fungal DNA was sequenced by ITS1 metagenomic analysis, and taxonomic classification was performed.<br><br>RESULTS: Data from samples collected from the antecubital fossa revealed that the &#x3b1; diversity of the skin mycobiome decreased significantly after treatment with anti-IL-23 antibodies (p&#xa0;=&#xa0;0.0120). Fungal DNAs were not amplified in 6/15 swab samples after 16 weeks of IL-23 inhibition; by contrast, sufficiently detected in all 15 samples before treatment (p&#xa0;=&#xa0;0.0554). A comparison of 9/15 paired samples containing well-detected reads revealed that the percentage of genus Malassezia in the mycobiome fell significantly after treatment with IL-23 inhibitors (before, 29.3%&#xa0;&#xb1;&#xa0;9.9%; after; 8.5%&#xa0;&#xb1;&#xa0;3.4%, p&#xa0;=&#xa0;0.0137). The mycobiome on post-auricular skin and on the tongue surface showed no marked changes after IL-23 inhibition.<br><br>CONCLUSIONS: Taken together, the data suggest that inhibition of systemic IL-23 provokes dysbiosis of the mycobiome at the antecubital fossa skin, a finding characterized by reduced fungal diversity and a reduction in the percentage of the genus Malassezia.},
}
@article {pmid39306935,
year = {2024},
author = {Liu, Y and Chen, H and Zhang, Y and Liu, C and Song, L},
title = {Metagenomics-resolved genomics provide novel ecological insights into resistome community coalescence of wastewater in river environment.},
journal = {Water research},
volume = {267},
number = {},
pages = {122473},
doi = {10.1016/j.watres.2024.122473},
pmid = {39306935},
issn = {1879-2448},
abstract = {The discharge of wastewater into rivers can lead to resistome coalescence, thereby enhancing the spread risk of antibiotic resistance genes (ARGs) through mixing of exogenous wastewater resistome communities with indigenous riverine communities. At present, the understanding on the role of resistome community coalescence in the dissemination of ARGs is still very limited, and little is known about the process and its ecological implications. To bridge the gap, this study has conducted field-based surveys and microcosm experiments to deeply dissect the coalescence of resistome community in wastewater within river environment, utilizing genome-centric metagenomic analysis approach. The field investigation suggests resistome coalescence enhances the abundance and diversity of ARGs in the receiving river. Furthermore, the microcosm experiments reveal the effect of mixing ratio on resistome coalescence in the water-sediment system and decipher the temporal attenuation dynamics of the coalesced resistome in the environment. The results show the higher proportion of wastewater has a greater impact on ARGs in the water, whereas the effect of mixing ratio is lesser in the sediments. Temporally, the source-specific ARGs originating from wastewater exhibit decreasing trends over the experimental duration, and relatively, the attenuation in the water is more pronounced than that in the sediments. Interestingly, natural light not only facilitates the attenuation of ARGs in the water but may also induce their deposition at the water-sediment interface. Variance partitioning analyses suggest the microbiome, mobilome, and abiotic factors collectively shape the coalescence of the resistome communities in the environment. The study provides empirical evidence on resistome coalescence in river systems, which is instrumental in gaining a better understanding of the spread mechanism of ARGs in the environment.},
}
@article {pmid39306821,
year = {2024},
author = {Yang, D and Zhang, C and Ge, S and Xie, Y and Yuan, L},
title = {Performance of single PN/A reactor under wide fluctuation of nitrogen load.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {39306821},
issn = {1614-7499},
support = {No.2019XKQYMS79//Fundamental Research Funds for the Central Universities/ ; No. 52270171//National Natural Science Foundation of China/ ; },
abstract = {Partial nitritation-anammox (PN/A) is a cost-effective technology in high ammonia-nitrogen wastewater treatment. However, PN/A is prone to instability as the ammonia-nitrogen sharply fluctuates. In this study, a packed bed reactor is employed to construct a single-stage PN/A system to investigate the operational characteristics and explore the denitrification mechanism. The effluent NH4[+]-N concentration, ammonia nitrogen removal rate (ARE), and total nitrogen removal rate (TNR) could be sustained at about 60 mg/L, 80%, and over 70%, respectively, when the influent nitrogen load rate (NLR) is changed from 0.733 to 0.879 kg-N/m[3]/day. Both ARE and TNR are decreased when NLR continues increasing to 1.026 kg-N/m[3]/day. The influent NLR decreases from 0.879 to 0.147 kg-N/m[3]/day, and ARE and TNR reached 98% and 85.4%, respectively. Therefore, the denitrification effect of the reactor could be recovered, and the excellent nitrogen removal capacity could be obtained within a wide range of influent NLR. Moreover, the high-throughput sequencing and metagenomic testing indicate that the Proteobacteria and Planctomycetes that the PN/A functional strains (i.e., ammonia-oxidizing bacteria (AOB) and anammox bacteria (AnAOB)) account for 38.8% in the sludge. The relative abundance of Nitrospira containing the nitrite-oxidizing bacteria (NOB) has dropped to 0.01%, and the functional gene nxr of the nitrite oxidation process is also inhibited. The relative expression of the functional gene is dominated by the short-range nitritation and anammox oxidation, which demonstrates that the nitrogen removal is mainly dominated by nitritation-anammox.},
}
@article {pmid39306820,
year = {2024},
author = {Li, J and Huang, W and Li, Q},
title = {New insights into pathogenic performances during peroxydisulfate composting: sources, pathways, and influencing factors.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {39306820},
issn = {1614-7499},
support = {21878057//National Natural Science Foundation of China/ ; },
abstract = {Livestock manure treatment technology and composting and its products have been widely used in agricultural soil. However, little was known about the variations in the fate of pathogens and the factors affecting their pathogenic ability during this process, which posed threats to ecological safety and public health globally. This study used a metagenomic approach to profile the behaviors of pathogens during peroxydisulfate composting. Results showed that Pseudomonas aeruginosa, Klebsiella pneumoniae, Escherichia coli, Burkholderia pseudomallei, and Mycobacterium tuberculosis were the main secretors of virulence factors (VFs) in composting system; their abundance and the virulence factor-related genes they carried were better downregulated under the role of peroxydisulfate. In addition, peroxydisulfate composting ensured the lower moisture, weakening the swimming mobility behavior of pathogens through suppressing the abundance of genes associated with flagellar formation, and impaired the communication between pathogens by regulating quorum sensing (QS)- and quorum quenching (QQ)-related genes. Moreover, reduced abundance of resistomes restricted pathogens disseminating infection. In summary, this study provided useful strategies in managing pathogen pathogenic ability during composting based on pathogenic source (pathogens), pathway (VFs), influencing factors (QS/QQ, physicochemical habitats), and resistomes.},
}
@article {pmid39306400,
year = {2025},
author = {Guo, F and Yan, G and Wang, H and Shi, L and Zhang, Y and Ling, Y and Wei, Y and Wang, H and Dong, W and Chang, Y and Tian, Z},
title = {Denitrification enhanced by composite carbon sources in AAO-biofilter: Efficiency and metagenomics research.},
journal = {Journal of environmental sciences (China)},
volume = {150},
number = {},
pages = {25-35},
doi = {10.1016/j.jes.2024.03.013},
pmid = {39306400},
issn = {1001-0742},
mesh = {*Denitrification ; *Carbon/metabolism ; *Metagenomics ; *Waste Disposal, Fluid/methods ; Nitrogen/metabolism ; Bioreactors ; Anaerobiosis ; Sewage ; Filtration/methods ; },
abstract = {Nitrogen removal from domestic sewage is usually limited by insufficient carbon source and electron donor. An economical solid carbon source was developed by composition of polyvinyl alcohol, sodium alginate, and corncob, which was utilized as external carbon source in the anaerobic anoxic oxic (AAO)-biofilter for the treatment of low carbon-to-nitrogen ratio domestic sewage, and the nitrogen removal was remarkably improved from 63.2% to 96.5%. Furthermore, the effluent chemical oxygen demand maintained at 35 mg/L or even lower, and the total nitrogen was reduced to less than 2 mg/L. Metagenomic analysis demonstrated that the microbial communities responsible for potential denitrification and organic matter degradation in both AAO and the biofilter reactors were mainly composed of Proteobacteria and Bacteroides, respectively. The solid carbon source addition resulted in relatively high abundance of functional enzymes responsible for NO3[-]-N to NO2[-]-N conversion in both AAO and the biofilter reactors, thus enabled stable reaction. The carbon source addition during glycolysis primarily led to the increase of genes associated with the metabolic conversion of fructose 1.6P2 to glycerol-3P The reactor maintained high abundance of genes related to the tricarboxylic acid cycle, and then guaranteed efficient carbon metabolism. The results indicate that the composite carbon source is feasible for denitrification enhancement of AAO-biofilter, which contribute to the theoretical foundation for practical nitrogen removal application.},
}
@article {pmid39306146,
year = {2024},
author = {Martínez-Aranzales, JR and Córdoba-Agudelo, M and Pérez-Jaramillo, JE},
title = {Fecal microbiome and functional prediction profiles of horses with and without crib-biting behavior: a comparative study.},
journal = {Journal of equine veterinary science},
volume = {},
number = {},
pages = {105198},
doi = {10.1016/j.jevs.2024.105198},
pmid = {39306146},
issn = {0737-0806},
abstract = {Crib-biting is a stereotyped oral behavior with poorly understood etiology and pathophysiology. The relationship between the gut microbiome and brain function has been described in behavioral disorders such as schizophrenia, depression and anxiety in humans. In horses, studies of behavioral problems and the microbiome are very limited. This study aimed to characterize the fecal microbiome and the predicted functional profile of horses with and without aerophagia. Fecal samples were collected from 12 Colombian Creole Horses of both sexes, divided into two groups: group 1, composed of six horses with crib-biting (3 females and 3 males), average body weight of 330±10 kg, age of 7.0±1.2 years and body condition score (BCS) of 5/9±1 and group 2, consisting of six horses without crib-biting (3 females and 3 males), average body weight of 335±5 kg, age 6.5±1 years and BCS of 6/9±1. From each horse in both groups fecal total DNA was obtained and 16S ribosomal RNA gene amplicons were sequenced to characterize the bacterial community structure. Community structure and differential abundance analyses revealed significant differences between the two conditions (p<0.05). Specifically, the fecal microbiota at the family level in crib-biting horses, showing a decrease in Bacteroidales and an increase in Bacillota and Clostridia, differed from that of healthy horses without crib-biting, consistent with findings from previous studies. Furthermore, metagenome prediction suggests metabolic profile changes in bacterial communities between both conditions in horses. Further studies are required to validate the role of the microbiota-gut-brain axis in the etiology of crib-biting and other abnormal and stereotyped behaviors.},
}
@article {pmid39305955,
year = {2024},
author = {Masuda, R and Phyu Thant, KP and Kawahara, K and Oki, H and Kadonosono, T and Kobayashi, Y and Koide, T},
title = {A yeast two-hybrid system to obtain triple-helical ligands from combinatorial random peptide libraries.},
journal = {The Journal of biological chemistry},
volume = {},
number = {},
pages = {107794},
doi = {10.1016/j.jbc.2024.107794},
pmid = {39305955},
issn = {1083-351X},
abstract = {Many bioactive proteins interact with collagen, recognizing amino acid sequences displayed on the triple helix. We report here a selection strategy to obtain triple-helical peptides that interact with the proteins from a combinatorial random library constructed in yeast cells. This system enables us to select them using the standard two-hybrid protocol, detecting interactions between triple-helical peptides and target proteins fused to the GAL4-activating and binding domains, respectively. The library was constructed having triple-helical peptides with a "host-guest" design in which host helix-stabilizing regions flanked guest random sequences. Using this system, we selected peptides that bind to pigment epithelium-derived factor (PEDF), a collagen-binding protein that shows anti-angiogenic and neurotrophic activities, from the libraries. Two-step selections from the total random library and subsequently from the second focused library yielded new PEDF-binding sequences that exhibited a comparable affinity to or more potent than that of the native PEDF-binding sequence in collagen. The obtained sequences also contained a variant of the PEDF-binding motif that did not match the known motif identified from the native collagen sequences. This combinatorial library system allows the chemical space of triple-helical peptides to be screened more widely than that found in native collagen, thus increasing the expectation of obtaining more specific and high-affinity peptides.},
}
@article {pmid39305900,
year = {2024},
author = {Liu, Q and Huang, B and Zhou, Y and Wei, Y and Li, Y and Li, B and Li, Y and Zhang, J and Qian, Q and Chen, R and Lyu, Z and Wang, R and Cao, Q and Xu, Q and Wang, Q and Miao, Q and You, Z and Lian, M and Gershwin, ME and Jin, Q and Xiao, X and Ma, X and Tang, R},
title = {Gut microbiome pattern impacts treatment response in primary biliary cholangitis.},
journal = {Med (New York, N.Y.)},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.medj.2024.08.003},
pmid = {39305900},
issn = {2666-6340},
abstract = {BACKGROUND: Primary biliary cholangitis (PBC) is a progressive autoimmune liver disease. An inadequate response to ursodeoxycholic acid (UDCA) poses a high risk of progression toward end-stage liver disease. Gut dysbiosis has been implicated in PBC. Here, we aimed to investigate microbial signatures that permit risk stratification and provide mechanistic insights into novel therapies for PBC.<br><br>METHODS: We prospectively recruited UDCA treatment-naive patients with PBC and performed metagenomic sequencing and metabolomic profiling using stool and serum samples obtained before (n&#xa0;= 132) and after (n&#xa0;= 59) treatment. PBC microbiome subtypes were identified using unsupervised machine learning methods and validated in two independent cohorts.<br><br>FINDINGS: PBC baseline metagenomes clustered into two community subtypes characterized by varying abundances of Clostridia taxa. Compared with Clostridia[low] microbiomes, Clostridia[high] microbiomes were more similar to healthy controls. Notably, patients in the Clostridia[low] subtype exhibited a 2-fold higher UDCA non-response rate compared to those in the Clostridia[high] subtype (41% vs. 20%, p&#xa0;= 0.015). Integrative analysis of metagenomic and metabolomic data revealed divergent functional modules and metabolic activities between the two metacommunities. In particular, anaerobic fermentation and the production of bioactive metabolites, including tryptophan derivatives and secondary bile acids, crucial for immune regulation and gut barrier maintenance, were markedly diminished in the Clostridia[low] subtype. Moreover, UDCA administration reconfigured the fecal microbial and metabolic profiles only in the Clostridia[high] group. Importantly, the microbiome subtypes and their associations with UDCA response were reproducible in two independent treatment-naive PBC cohorts.<br><br>CONCLUSIONS: Characterizing baseline microbiota patterns may enable the prediction of treatment outcomes in PBC and facilitate personalized treatment strategies.<br><br>FUNDING: This research was mainly supported by the National Natural Science Foundation of China.},
}
@article {pmid39305897,
year = {2024},
author = {Zampirolo, G and Holman, LE and Sawafuji, R and Ptáková, M and Kovačiková, L and Šída, P and Pokorný, P and Pedersen, MW and Walls, M},
title = {Tracing early pastoralism in Central Europe using sedimentary ancient DNA.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2024.08.047},
pmid = {39305897},
issn = {1879-0445},
abstract = {Central European forests have been shaped by complex human interactions throughout the Holocene, with significant changes following the introduction of domesticated animals in the Neolithic (∼7.5-6.0 ka before present [BP]). However, understanding early pastoral practices and their impact on forests is limited by methods for detecting animal movement across past landscapes. Here, we examine ancient sedimentary DNA (sedaDNA) preserved at the Velký Mamuťák rock shelter in northern Bohemia (Czech Republic), which has been a forested enclave since the early Holocene. We find that domesticated animals, their associated microbiomes, and plants potentially gathered for fodder have clear representation by the Late Neolithic, around 6.0 ka BP, and persist throughout the Bronze Age into recent times. We identify a change in dominant grazing species from sheep to pigs in the Bronze Age (∼4.1-3.0 ka BP) and interpret the impact this had in the mid-Holocene retrogressions that still define the structure of Central European forests today. This study highlights the ability of ancient metagenomics to bridge archaeological and paleoecological methods and provide an enhanced perspective on the roots of the "Anthropocene."},
}
@article {pmid39305601,
year = {2024},
author = {Wang, F and Hu, Z and Wang, W and Wang, J and Xiao, Y and Shi, J and Wang, C and Mai, W and Li, G and An, T},
title = {Selective enrichment of high-risk antibiotic resistance genes and priority pathogens in freshwater plastisphere: Unique role of biodegradable microplastics.},
journal = {Journal of hazardous materials},
volume = {480},
number = {},
pages = {135901},
doi = {10.1016/j.jhazmat.2024.135901},
pmid = {39305601},
issn = {1873-3336},
abstract = {Microplastics (MPs) has been concerned as emerging vectors for spreading antibiotic resistance and pathogenicity in aquatic environments, but the role of biodegradable MPs remains largely unknown. Herein, field in-situ incubation method combined with metagenomic sequencing were employed to reveal the dispersal characteristics of microbial community, antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and virulence factors (VFs) enriched by MPs biofilms. Results showed that planktonic microbes were more prone to enrich on biodegradable MPs (i.e., polyhydroxyalkanoate and polylactic acid) than non-biodegradable MPs (i.e., polystyrene, polypropylene and polyethylene). Distinctive microbial communities were assembled on biodegradable MPs, and the abundances of ARGs, MGEs, and VFs on biofilms of biodegradable MPs were much higher than that of non-biodegradable MPs. Notably, network analysis showed that the biodegradable MPs selectively enriched pathogens carrying ARGs, VFs and MGEs concurrently, suggesting a strong potential risks of co-spreading antibiotic resistance and pathogenicity through horizontal gene transfer. According to WHO priority list of Antibiotic Resistant Pathogens (ARPs) and ARGs health risk assessment framework, the highest abundances of Priority 1 ARPs and Rank I risk ARGs were found on polylactic acid and polyhydroxyalkanoate, respectively. These findings elucidate the unique and critical role of biodegradable MPs for selective enrichment of high-risk ARGs and priority pathogens in freshwater environments.},
}
@article {pmid39305563,
year = {2024},
author = {Albuquerque, L and Viver, T and Barroso, C and Claudino, R and Galvan, M and Simões, G and Lobo-da-Cunha, A and Egas, C},
title = {Halorubrum miltondacostae sp. nov., a potential polyhydroxyalkanoate producer isolated from an inland solar saltern in Rio Maior, Portugal.},
journal = {Systematic and applied microbiology},
volume = {47},
number = {6},
pages = {126553},
doi = {10.1016/j.syapm.2024.126553},
pmid = {39305563},
issn = {1618-0984},
abstract = {One hundred and sixty-three extreme halophiles were recovered from a single sample collected from an inland solar saltern in Rio Maior. Based on random amplified polymorphic DNA (RAPD) profiles and partial 16S rRNA gene sequencing 125 isolates were identified as members of the Archaea domain within the genus Halorubrum. Two strains, RMP-11[T] and RMP-47, showed 99.1 % sequence similarity with the species Halorubrum californiense based on phylogenetic analysis of the 16S rRNA gene sequence. However, phylogenetic analysis based on five housekeeping genes, atpB, EF-2, glnA, ppsA and rpoB', showed Halorubrum coriense as the closest related species with 96.7 % similarity. The average nucleotide identity (ANI) of strains RMP-11[T], RMP-47 and species Hrr. coriense were within the range of 90.0-90.5 %, supporting that strains RMP-11[T] and RMP-47 represent a novel species of the genus Halorubrum. These strains formed red-pigmented colonies that were able to grow in a temperature range of 25-50 °C. Polyhydroxyalkanoate (PHA) granules were detected in both strains. The polar lipid profile was identical to the neutrophilic species of the genus Halorubrum. The Rio Maior sample from which both strains were isolated was metagenome sequenced. We identified five metagenome-assembled genomes representing novel Halorubrum species but distinct from the species represented by strains RMP-11[T] and RMP-47. Based on phylogenetic, phylogenomic, comparative genomics, physiological and chemotaxonomic parameters, we describe a new species of the genus Halorubrum represented by strains RMP-11[T] (=CECT 30760[T] = DSM 115521[T]) and RMP-47 (=CECT 30761 = DSM 115541) for which we propose the name Halorubrum miltondacostae sp. nov.},
}
@article {pmid39305530,
year = {2024},
author = {Jiang, H and Jiang, M and Zhang, Q},
title = {Coupled sulfur and nitrogen cycling at a catchment scale: insights from isotopic and molecular techniques.},
journal = {Water research},
volume = {267},
number = {},
pages = {122438},
doi = {10.1016/j.watres.2024.122438},
pmid = {39305530},
issn = {1879-2448},
abstract = {The biogeochemical cycles of nitrogen (N) and sulfur (S) play important roles in sustaining the Earth's ecosystem. However, their potential coupling process and underlying mechanisms in the nature remain unclear. Through joint applications of river water's isotopic compositions, isotope-pairing experiments, and molecular techniques, this study revealed the coupled N-S cycling processes at a catchment scale from both geochemical and biological perspectives. The river water's natural abundance isotopic compositions indicated that sulfide oxidation was an important source (67.0 ± 5.5 % in summer and 72.0 ± 5.5 % in winter) of riverine sulfate (SO4[2-]). In addition, sulfide oxidation and NOx reduction (especially denitrification) were tightly coupled in summer but less significantly so in winter. However, the coupling of sulfide oxidation and dissimilatory nitrate reduction to ammonium (DNRA) could not be overlooked in winter. The [15]N pairing experiments quantitatively showed that the high sulfide oxidation rates in summer (4.7 ± 2.3 mol/km[2]/h) were significantly associated with the denitrification. Metagenomics and qPCR analyses of the soils supported the isotopic interpretations, substantiating the metabolic potential and coexistence of bacterial denitrification, DNRA, and sulfide oxidation, which was more prevalent in summer. This study reveals comprehensive evidence that sulfide oxidation and NOx reduction are tightly coupled at the catchment scale, which provides a new perspective towards a better understanding of N-S cycling.},
}
@article {pmid39304820,
year = {2024},
author = {Silva, MH and Batista, LL and Malta, SM and Santos, ACC and Mendes-Silva, AP and Bonetti, AM and Ueira-Vieira, C and Dos Santos, AR},
title = {Unveiling the Brazilian kefir microbiome: discovery of a novel Lactobacillus kefiranofaciens (LkefirU) genome and in silico prospection of bioactive peptides with potential anti-Alzheimer properties.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {884},
pmid = {39304820},
issn = {1471-2164},
mesh = {*Kefir/microbiology ; *Alzheimer Disease ; *Lactobacillus/genetics ; *Genome, Bacterial ; *Microbiota ; Brazil ; *Peptides/chemistry/pharmacology ; Humans ; Molecular Docking Simulation ; Amyloid beta-Peptides/metabolism/genetics ; Amyloid Precursor Protein Secretases/metabolism ; Aspartic Acid Endopeptidases/genetics/metabolism ; Metagenomics/methods ; },
abstract = {BACKGROUND: Kefir is a complex microbial community that plays a critical role in the fermentation and production of bioactive peptides, and has health-improving properties. The composition of kefir can vary by geographic localization and weather, and this paper focuses on a Brazilian sample and continues previous work that has successful anti-Alzheimer properties. In this study, we employed shotgun metagenomics and peptidomics approaches to characterize Brazilian kefir further.<br><br>RESULTS: We successfully assembled the novel genome of Lactobacillus kefiranofaciens (LkefirU) and conducted a comprehensive pangenome analysis to compare it with other strains. Furthermore, we performed a peptidome analysis, revealing the presence of bioactive peptides encrypted by L. kefiranofaciens in the Brazilian kefir sample, and utilized in silico prospecting and molecular docking techniques to identify potential anti-Alzheimer peptides, targeting &#x3b2;-amyloid (fibril and plaque), BACE, and acetylcholinesterase. Through this analysis, we identified two peptides that show promise as compounds with anti-Alzheimer properties.<br><br>CONCLUSIONS: These findings not only provide insights into the genome of L. kefiranofaciens but also serve as a promising prototype for the development of novel anti-Alzheimer compounds derived from Brazilian kefir.},
}
@article {pmid39304351,
year = {2024},
author = {Jiménez, DJ and Chaparro, D and Sierra, F and Custer, GF and Feuerriegel, G and Chuvochina, M and Diaz-Garcia, L and Mendes, LW and Ortega Santiago, YP and Rubiano-Labrador, C and Salcedo Galan, F and Streit, WR and Dini-Andreote, F and Reyes, A and Rosado, AS},
title = {Engineering the mangrove soil microbiome for selection of polyethylene terephthalate-transforming bacterial consortia.},
journal = {Trends in biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tibtech.2024.08.013},
pmid = {39304351},
issn = {1879-3096},
abstract = {Mangroves are impacted by multiple environmental stressors, including sea level rise, erosion, and plastic pollution. Thus, mangrove soil may be an excellent source of as yet unknown plastic-transforming microorganisms. Here, we assess the impact of polyethylene terephthalate (PET) particles and seawater intrusion on the mangrove soil microbiome and report an enrichment culture experiment to artificially select PET-transforming microbial consortia. The analysis of metagenome-assembled genomes of two bacterial consortia revealed that PET catabolism can be performed by multiple taxa, of which particular species harbored putative novel PET-active hydrolases. A key member of these consortia (Mangrovimarina plasticivorans gen. nov., sp. nov.) was found to contain two genes encoding monohydroxyethyl terephthalate hydrolases. This study provides insights into the development of strategies for harnessing soil microbiomes, thereby advancing our understanding of the ecology and enzymology involved in microbial-mediated PET transformations in marine-associated systems.},
}
@article {pmid39304154,
year = {2024},
author = {Wang, Q and Liu, M and Huang, J and Han, C and Jiang, Y and Deng, H and Liu, K and Zhong, W},
title = {Organic manure rather than chemical fertilization improved dark CO2 fixation by regulating associated microbial functional traits in upland red soils.},
journal = {The Science of the total environment},
volume = {954},
number = {},
pages = {176337},
doi = {10.1016/j.scitotenv.2024.176337},
pmid = {39304154},
issn = {1879-1026},
abstract = {Dark microbial fixation of CO2 is an indispensable process for soil carbon sequestration. However, the whole genetic information involved in dark CO2 fixation and its influence on dark CO2 fixation rates under diversified fertilization regimes were largely unclear. Here, revealed by [13]C-CO2 labeling, dark CO2 fixation rates in upland red soils ranged from 0.029 mg kg[-1] d[-1] to 0.092 mg kg[-1] d[-1], and it was 75.49 % higher (P < 0.05) in organic manure (OM) soil but 44.2 % decline (P < 0.05) in chemical nitrogen fertilizer (N) soil compared to unfertilized (CK) soil. In addition, the normalized abundance and Chao1 index of dark CO2 fixation genes (KO level) were significantly different between OM and N soils, showing the highest and lowest, respectively. And they were positively (P < 0.05) correlated with dark CO2 fixation rate. Besides, among the identified CO2 fixation pathways in this study, the DC/4-HB cycle (M00374) was enriched in OM soil, yet the 3-HP cycle (M00376) was enriched in N soil, and their relative abundances were positively and negatively correlated (P < 0.05) with dark CO2 fixation rate, respectively. The PLS-SEM analysis revealed that dark CO2 fixation-related functional traits (i.e. normalized abundance, Chao1 index and gene composition) were directly and positively associated with dark CO2 fixation rate, and organic manure could exert a positive effect on soil dark CO2 fixation rate through enhancing soil properties (e.g., pH and soil organic carbon) and further altering associated microbial functional traits. These results have implications for explaining and predicting the soil CO2 fixation process from the perspective of microbial functional potential.},
}
@article {pmid39303948,
year = {2024},
author = {Xu, M and Chen, HQ and Gao, P and Shen, XX},
title = {Fulvic acid impact on constructed wetland-microbial electrolysis cell system performance: Metagenomic insights.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {131504},
doi = {10.1016/j.biortech.2024.131504},
pmid = {39303948},
issn = {1873-2976},
abstract = {This study explores the roles of fulvic acid (FA) in both a conventionally constructed wetland (CCW) and a newly constructed wetland-microbial electrolysis cell (ECW). The results showed that FA increased the average removal efficiency of chemical oxygen demand, total phosphorus, total nitrogen, and ammonia nitrogen in ECW by 8.6, 46.2, 33.0, and 27.9 %, respectively, compared to CCW, and reduced the global warming potential by > 60 %. FA promoted the proliferation of electroactive bacteria (e.g., Chlorobaculum and Candidatus Tenderia) and FA-degrading bacteria (e.g., Anaerolineaceae and Gammaproteobacteria) and reduced methanogens (e.g., Methanothrix) via type-changing. The study's findings suggest that FA influences pollutant removal and microbiome dynamics by altering dissolved oxygen levels and redox potential. In summary, FA and ECW enhanced the efficiency of constructed wetlands by facilitating electron transfer and consumption, and supporting microbial growth and metabolism.},
}
@article {pmid39303692,
year = {2024},
author = {Crits-Christoph, A and Levy, JI and Pekar, JE and Goldstein, SA and Singh, R and Hensel, Z and Gangavarapu, K and Rogers, MB and Moshiri, N and Garry, RF and Holmes, EC and Koopmans, MPG and Lemey, P and Peacock, TP and Popescu, S and Rambaut, A and Robertson, DL and Suchard, MA and Wertheim, JO and Rasmussen, AL and Andersen, KG and Worobey, M and Débarre, F},
title = {Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic.},
journal = {Cell},
volume = {187},
number = {19},
pages = {5468-5482.e11},
doi = {10.1016/j.cell.2024.08.010},
pmid = {39303692},
issn = {1097-4172},
mesh = {Animals ; *COVID-19/epidemiology/virology ; *SARS-CoV-2/genetics/isolation &amp; purification ; *Animals, Wild/virology ; *Phylogeny ; Humans ; Pandemics ; },
abstract = {Zoonotic spillovers of viruses have occurred through the animal trade worldwide. The start of the COVID-19 pandemic was traced epidemiologically to the Huanan Seafood Wholesale Market. Here, we analyze environmental qPCR and sequencing data collected in the Huanan market in early 2020. We demonstrate that market-linked severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genetic diversity is consistent with market emergence and find increased SARS-CoV-2 positivity near and within a wildlife stall. We identify wildlife DNA in all SARS-CoV-2-positive samples from this stall, including species such as civets, bamboo rats, and raccoon dogs, previously identified as possible intermediate hosts. We also detect animal viruses that infect raccoon dogs, civets, and bamboo rats. Combining metagenomic and phylogenetic approaches, we recover genotypes of market animals and compare them with those from farms and other markets. This analysis provides the genetic basis for a shortlist of potential intermediate hosts of SARS-CoV-2 to prioritize for serological and viral sampling.},
}
@article {pmid39303598,
year = {2024},
author = {Wu, T and Ding, J and Sun, HJ and Pang, JW and Zhong, L and Zhao, L and Zhang, LY and Ren, NQ and Yang, SS},
title = {Deciphering the roles of attached and suspended sludges in simultaneous nitrogen and phosphorus removal in an IFAS system based on metagenomic analysis.},
journal = {Journal of environmental management},
volume = {370},
number = {},
pages = {122567},
doi = {10.1016/j.jenvman.2024.122567},
pmid = {39303598},
issn = {1095-8630},
abstract = {Integrated fixed-film activated sludge (IFAS) system, an improvement of the activated sludge process, combines the advantages of both attached sludge (AS) and suspended sludge (SS). This study aimed to fully decipher the roles of AS and SS in simultaneous N and P removal in an IFAS system through metagenomic analysis. It was found that AS contributed about 84.04%, 97%, and 95.12% to exogenous NO3[-]-N reduction, endogenous NO3[-]-N reduction, and endogenous NO2[-]-N reduction, respectively. Compared with AS, SS exhibited a greater contribution to anaerobic P release (69.06%) and aerobic P uptake (73.48%). Nitrate and nitrite reductase enzymes showed higher activities in AS, while the activities of exopolyphosphatase and alkaline phosphatase D were more active in SS. P content further indicated that in AS, only a small amount of P was stored in EPS, with most presented intracellularly. In SS, the amount of P stored in EPS was found to be higher. Metagenomic analysis revealed genes related to the synthesis and degradation of endogenous carbon were higher in AS, whereas the TCA cycle exhibited higher activity in SS. P removal-related genes (such as ppk2, ppx, and adk) was significantly higher in SS than in AS. The alteration of genes associated with nitrogen metabolism suggested that the microbes in AS had a higher capacity for nitrification and denitrification. In summary, the discrepancy in the roles of AS and SS in N and P removal in IFAS can be attributed to variations in enzyme activity, P storage in EPS, microbial community composition, and functional gene abundance.},
}
@article {pmid39303414,
year = {2024},
author = {Sipes, K and Buongiorno, J and Steen, AD and Abramov, AA and Abuah, C and Peters, SL and Gianonne, RJ and Hettich, RL and Boike, J and Garcia, SL and Vishnivetskaya, TA and Lloyd, KG},
title = {Depth-specific distribution of bacterial MAGs in permafrost active layer in Ny Ålesund, Svalbard (79°N).},
journal = {Systematic and applied microbiology},
volume = {47},
number = {6},
pages = {126544},
doi = {10.1016/j.syapm.2024.126544},
pmid = {39303414},
issn = {1618-0984},
abstract = {Arctic soil microbial communities may shift with increasing temperatures and water availability from climate change. We examined temperature and volumetric liquid water content (VWC) in the upper 80 cm of permafrost-affected soil over 2 years (2018-2019) at the Bayelva monitoring station, Ny Ålesund, Svalbard. We show VWC increases with depth, whereas in situ temperature is more stable vertically, ranging from -5°C to 5 °C seasonally. Prokaryotic metagenome-assembled genomes (MAGs) were obtained at 2-4 cm vertical resolution collected while frozen in April 2018 and at 10 cm vertical resolution collected while thawed in September 2019. The most abundant MAGs were Acidobacteriota, Actinomycetota, and Chloroflexota. Actinomycetota and Chloroflexota increase with depth, while Acidobacteriota classes Thermoanaerobaculia Gp7-AA8, Blastocatellia UBA7656, and Vicinamibacteria Vicinamibacterales are found above 6 cm, below 6 cm, and below 20 cm, respectively. All MAGs have diverse carbon-degrading genes, and Actinomycetota and Chloroflexota have autotrophic genes. Genes encoding β -glucosidase, N-acetyl-β-D-glucosaminidase, and xylosidase increase with depth, indicating a greater potential for organic matter degradation with higher VWC. Acidobacteriota dominate the top 6 cm with their classes segregating by depth, whereas Actinomycetota and Chloroflexota dominate below ∼6 cm. This suggests that Acidobacteriota classes adapt to lower VWC at the surface, while Actinomycetota and Chloroflexota persist below 6 cm with higher VWC. This indicates that VWC may be as important as temperature in microbial climate change responses in Arctic mineral soils. Here we describe MAG-based Seqcode type species in the Acidobacteriota, Onstottus arcticum, Onstottus frigus, and Gilichinskyi gelida and in the Actinobacteriota, Mayfieldus profundus.},
}
@article {pmid39301264,
year = {2024},
author = {Zhao, Y and Ma, S and Liang, L and Cao, S and Fan, Z and He, D and Shi, X and Zhang, Y and Liu, B and Zhai, M and Wu, S and Kuang, F and Zhang, H},
title = {Gut Microbiota-Metabolite-Brain Axis Reconstitution Reverses Sevoflurane-Induced Social and Synaptic Deficits in Neonatal Mice.},
journal = {Research (Washington, D.C.)},
volume = {7},
number = {},
pages = {0482},
pmid = {39301264},
issn = {2639-5274},
abstract = {Background: The mechanisms underlying social dysfunction caused by repeated sevoflurane in early life remain unclear. Whether the gut microbiota-metabolite-brain axis is involved in the mechanism of sevoflurane developmental neurotoxicity still lacks report. Methods: Mice received 3% sevoflurane at postnatal day (PND) 6, 7, and 8 for 2 h per day. Metagenomic sequencing and untargeted metabolomic analysis were applied to investigate the effects of sevoflurane on gut microbiota and metabolism. The animal social behavior and the synaptic development were analyzed during PND 35. Subsequently, fecal microbiota transplantation (FMT) from the control group and bile acid administration were performed to see the expected rescuing effect on socially related behaviors that were impaired by repeated sevoflurane exposure in the mice. Results: In the 3-chamber test, sevoflurane-exposed mice spent less time with stranger mice compared with the control group. The density of both the apical and basal spine decreased in mice exposed to sevoflurane. In addition, repeated sevoflurane exposure led to a notable alteration in the gut microbiota and metabolite synthesis, particularly bile acid. FMT reduced the production of intestinal bile acid and attenuated the effect of sevoflurane exposure on social function and synaptic development. Cholestyramine treatment mimics the protective effects of FMT. Conclusions: The gut microbiota-metabolite-brain axis underlies social dysfunction caused by sevoflurane exposure in early age, and bile acid regulation may be a promising intervention to this impairment.},
}
@article {pmid39301212,
year = {2024},
author = {Nong, Y and Walsh, DM and Maloh, J and Dadlani, M and Sivamani, R},
title = {Whole-Genome Shotgun Metagenomic Sequencing Reveals Shifts in the Skin Microbiome and Bacteriophages of Psoriasis: An Extended Analysis of Published Data.},
journal = {Journal of psoriasis and psoriatic arthritis},
volume = {9},
number = {3},
pages = {98-107},
pmid = {39301212},
issn = {2475-5311},
abstract = {BACKGROUND: Psoriasis is an immune-mediated cutaneous disease that may have shifts in the skin microbiome. Prior research on the skin microbiome in psoriasis has been limited to rRNA based approaches that lack resolution of taxonomic and functional level assessment.<br><br>OBJECTIVE: To further illuminate strain and sub-strain level analysis of psoriatic lesions using the CosmosID-HUB Microbiome pipeline.<br><br>METHODS: A previous study completed by Tett et al recruited patients with psoriasis who had skin microbiome samples taken from psoriatic plaques on the ear and the elbow as well as sites on the skin unaffected by psoriasis. They performed whole genome shotgun sequencing and made their dataset publicly available. We analyzed the dataset using the CosmosID-HUB Microbiome pipeline to evaluate the strain and sub-strain taxonomic analysis as well as functional gene profiling.<br><br>RESULTS: When analyzed with the CosmosID pipeline, both ear and elbow sites in affected areas had decreased alpha diversity compared to unaffected areas. There was an increased relative abundance of Staphylococcus and Corynebacteria at affected sites. We identified distinguishing species and strains of the yeast Malassezia, including M. restricta. that were significantly enriched in healthy elbow samples. Vitamin B12 production genes were not present in psoriatic skin whereas it was present in healthy samples, supporting the notion of relative vitamin B12 deficiency in psoriatic plaques. Phage analysis revealed a greater diversity of Staphylococcus-related phages in unaffected elbow samples.<br><br>CONCLUSION: A greater diversity of microbial strains and their functional roles identified in this study may help to tailor treatment for psoriasis.},
}
@article {pmid39303138,
year = {2024},
author = {Boukheloua, R and Mukherjee, I and Park, H and Šimek, K and Kasalický, V and Ngochera, M and Grossart, HP and Picazo-Mozo, A and Camacho, A and Cabello-Yeves, PJ and Rodriguez-Valera, F and Callieri, C and Andrei, AS and Pernthaler, J and Posch, T and Alfreider, A and Sommaruga, R and Hahn, MW and Sonntag, B and Lopez-Garcia, P and Moreira, D and Jardillier, L and Lepère, C and Biderre-Petit, C and Bednarska, A and Ślusarczyk, M and Tóth, VR and Banciu, HL and Kormas, K and Orlic, S and Šantić, D and Muyzer, G and Herlemann, DPR and Tammert, H and Bertilsson, S and Langenheder, S and Zechmeister, T and Salmaso, N and Storelli, N and Capelli, C and Lepori, F and Lanta, V and Vieira, HH and Kostanjšek, F and Kabeláčová, K and Chiriac, MC and Haber, M and Shabarova, T and Fernandes, C and Rychtecký, P and Znachor, P and Szőke-Nagy, T and Layoun, P and Wong, HL and Kavagutti, VS and Bulzu, PA and Salcher, MM and Piwosz, K and Ghai, R},
title = {Global freshwater distribution of Telonemia protists.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae177},
pmid = {39303138},
issn = {1751-7370},
abstract = {Telonemia are one of the oldest identified marine protists that for most part of their history have been recognized as a distinct incertae sedis lineage. Today, their evolutionary proximity to the SAR supergroup (Stramenopiles, Alveolates, and Rhizaria) is firmly established. However, their ecological distribution and importance as a natural predatory flagellate, especially in freshwater food webs, still remains unclear. To unravel the distribution and diversity of the phylum Telonemia in freshwater habitats, we examined over a thousand freshwater metagenomes from all over the world. In addition, to directly quantify absolute abundances, we analysed 407 samples from 97 lakes and reservoirs using Catalyzed Reporter Deposition-Fluorescence in situ Hybridization (CARD-FISH). We recovered Telonemia 18S rRNA gene sequences from hundreds of metagenomic samples from a wide variety of habitats, indicating a global distribution of this phylum. However, even after this extensive sampling, our phylogenetic analysis did not reveal any new major clades, suggesting current molecular surveys are near to capturing the full diversity within this group. We observed excellent concordance between CARD-FISH analyses and estimates of abundances from metagenomes. Both approaches suggest that Telonemia are largely absent from shallow lakes and prefer to inhabit the colder hypolimnion of lakes and reservoirs in the Northern Hemisphere, where they frequently bloom, reaching 10-20% of the total heterotrophic flagellate population, making them important predatory flagellates in the freshwater food web.},
}
@article {pmid39303118,
year = {2024},
author = {Doré, J and Sansonetti, PJ},
title = {[The human microbiome: 340 years of history, 140 years of interrogations, technological innovations and emergence of "microbial medicine"].},
journal = {Medecine sciences : M/S},
volume = {40},
number = {8-9},
pages = {654-660},
doi = {10.1051/medsci/2024101},
pmid = {39303118},
issn = {1958-5381},
mesh = {Humans ; *Microbiota/physiology ; History, 20th Century ; History, 21st Century ; History, 19th Century ; Symbiosis ; Inventions/history/trends ; History, 18th Century ; Gastrointestinal Microbiome/physiology ; },
abstract = {For 350 years, we have known that the human body hosts microbes, then called "animalcules". For over a century, following the demonstration of the role of some of these microbes in diseases, questions have arisen about the role of the largely predominant ones colonizing human skin and mucous surfaces, particularly the rich microbial ecosystem of the intestine, the gut microbiota. From the invention of germ-free life - axenism - which experimentally validated the human-microbe symbiosis, resulting from a long coevolution, to the development of anaerobic culture methods, then to the invention of molecular diagnosis, deep sequencing opening up metagenomic and omics approaches in general, a remarkable race has taken place between technological innovations and conceptual advances. This race, beyond the exhaustive description of the microbiota in its intra- and inter-human diversity, and the essential symbiotic functions of the microbiome, has paved the way for a new field of medicine: microbial medicine.},
}
@article {pmid39302083,
year = {2024},
author = {Cui, Y and Pan, D and Feng, J and Zhao, D and Liu, M and Dong, Z and Liu, S and Wang, S},
title = {Untargeted Metabolomics and Soil Community Metagenomics Analyses Combined with Machine Learning Evaluation Uncover Geographic Differences in Ginseng from Different Locations.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.4c04708},
pmid = {39302083},
issn = {1520-5118},
abstract = {Panax ginseng C.A. Meyer, known as the "King of Herbs," has been used as a nutritional supplement for both food and medicine with the functions of relieving fatigue and improving immunity for thousands of years in China. In agricultural planting, soil environments of different geographical origins lead to obvious differences in the quality of ginseng, but the potential mechanism of the differences remains unclear. In this study, 20 key differential metabolites, including ginsenoside Rb1, glucose 6-phosphate, etc., were found in ginseng from 10 locations in China using an ultra-high performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UHPLC-QTOF-MS)-untargeted metabolomics approach. The soil properties were analyzed and combined with metagenomics technology to explore the possible relationships among microbial elements in planting soil. Through Spearman correlation analysis, it was found that the top 10 microbial colonies with the highest abundance in the soil were significantly correlated with key metabolites. In addition, the relationship model established by the random forest algorithm and the quantitative relationship between soil microbial abundance and ginseng metabolites were successfully predicted. The XGboost model was used to determine 20(R)-ginseng Rg2 and 2'(R)-ginseng Rg3 as feature labeled metabolites, and the optimal ginseng production area was discovered. These results prove that the accumulation of metabolites in ginseng was influenced by microorganisms in the planting soil, which led to geographical differences in ginseng quality.},
}
@article {pmid39300577,
year = {2024},
author = {Lezcano, M&#xc1; and Bornemann, TLV and Sánchez-García, L and Carrizo, D and Adam, PS and Esser, SP and Cabrol, NA and Probst, AJ and Parro, V},
title = {Hyperexpansion of genetic diversity and metabolic capacity of extremophilic bacteria and archaea in ancient Andean lake sediments.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {176},
pmid = {39300577},
issn = {2049-2618},
support = {FJC2018-037246-I//Spanish Ministry of Science and Innovation/State Agency of Research/ ; RYC2018-023943-I//Spanish Ministry of Science and Innovation/State Agency of Research/ ; RYC-2014-19446//Spanish Ministry of Science and Innovation/State Agency of Research/ ; RTI2018-094368-B-I0//Spanish Ministry of Science and Innovation/State Agency of Research/ ; PEJD-2017- POST/TIC-4119//Spanish Ministry of Science and Innovation/State Agency of Research (EU Youth Employment Initiative)/ ; NAI-CAN7, 13NAI7_2-0018//NASA Astrobiology Institute/ ; DFG PR1603/2-1//German Research Foundation/ ; 161L0285E//German Federal Ministry of Education and Research/ ; },
mesh = {*Lakes/microbiology ; *Archaea/genetics/metabolism/classification ; *Geologic Sediments/microbiology ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Genetic Variation ; Chile ; Phylogeny ; Microbiota ; Extremophiles/metabolism/genetics/classification ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: The Andean Altiplano hosts a repertoire of high-altitude lakes with harsh conditions for life. These lakes are undergoing a process of desiccation caused by the current climate, leaving terraces exposed to extreme atmospheric conditions and serving as analogs to Martian paleolake basins. Microbiomes in Altiplano lake terraces have been poorly studied, enclosing uncultured lineages and a great opportunity to understand environmental adaptation and the limits of life on Earth. Here we examine the microbial diversity and function in ancient sediments (10.3-11 kyr BP (before present)) from a terrace profile of Laguna Lejía, a sulfur- and metal/metalloid-rich saline lake in the Chilean Altiplano. We also evaluate the physical and chemical changes of the lake over time by studying the mineralogy and geochemistry of the terrace profile.<br><br>RESULTS: The mineralogy and geochemistry of the terrace profile revealed large water level fluctuations in the lake, scarcity of organic carbon, and high concentration of SO4[2-]-S, Na, Cl and Mg. Lipid biomarker analysis indicated the presence of aquatic/terrestrial plant remnants preserved in the ancient sediments, and genome-resolved metagenomics unveiled a diverse prokaryotic community with still active microorganisms based on in silico growth predictions. We reconstructed 591 bacterial and archaeal metagenome-assembled genomes (MAGs), of which 98.8% belonged to previously unreported species. The most abundant and widespread metabolisms among MAGs were the reduction and oxidation of S, N, As, and halogenated compounds, as well as aerobic CO oxidation, possibly as a key metabolic trait in the organic carbon-depleted sediments. The broad redox and CO2 fixation pathways among phylogenetically distant bacteria and archaea extended the knowledge of metabolic capacities to previously unknown taxa. For instance, we identified genomic potential for dissimilatory sulfate reduction in Bacteroidota and &#x3b1;- and &#x3b3;-Proteobacteria, predicted an enzyme for ammonia oxidation in a novel Actinobacteriota, and predicted enzymes of the Calvin-Benson-Bassham cycle in Planctomycetota, Gemmatimonadota, and Nanoarchaeota.<br><br>CONCLUSIONS: The high number of novel bacterial and archaeal MAGs in the Laguna Lej&#xed;a indicates the wide prokaryotic diversity discovered. In addition, the detection of genes in unexpected taxonomic groups has significant implications for the expansion of microorganisms involved in the biogeochemical cycles of carbon, nitrogen, and sulfur. Video Abstract.},
}
@article {pmid39300575,
year = {2024},
author = {Li, Q and Ruscheweyh, HJ and Østergaard, LH and Libertella, M and Simonsen, KS and Sunagawa, S and Scoma, A and Schwab, C},
title = {Trait-based study predicts glycerol/diol dehydratases as a key function of the gut microbiota of hindgut-fermenting carnivores.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {178},
pmid = {39300575},
issn = {2049-2618},
support = {9152//EMBO/ ; AUFF-F-2020-7//Aarhus Universitet Forsknings Fonden/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Feces/microbiology ; *Fermentation ; *Glycerol/metabolism ; *Metagenomics/methods ; Hydro-Lyases/genetics/metabolism ; Propylene Glycols/metabolism ; Vitamin B 12/metabolism ; Bacteria/classification/genetics/isolation &amp; purification/enzymology ; Phylogeny ; Animals, Wild/microbiology ; },
abstract = {BACKGROUND: Microbial pdu and cob-cbi-hem gene clusters encode the key enzyme glycerol/diol dehydratase (PduCDE), which mediates the transformation of dietary nutrients glycerol and 1,2-propanediol (1,2-PD) to a variety of metabolites, and enzymes for cobalamin synthesis, a co-factor and shared good of microbial communities. It was the aim of this study to relate pdu as a multipurpose functional trait to environmental conditions and microbial community composition. We collected fecal samples from wild animal species living in captivity with different gut physiology and diet (n = 55, in total 104 samples), determined occurrence and diversity of pdu and cob-cbi-hem using a novel approach combining metagenomics with quantification of metabolic and genetic biomarkers, and conducted in vitro fermentations to test for trait-based activity.<br><br>RESULTS: Fecal levels of the glycerol transformation product 1,3-propanediol (1,3-PD) were higher in hindgut than foregut fermenters. Gene-based analyses indicated that pduC harboring taxa are common feature of captive wild animal fecal microbiota that occur more frequently and at higher abundance in hindgut fermenters. Phylogenetic analysis of genomes reconstructed from metagenomic sequences identified captive wild animal fecal microbiota as taxonomically rich with a total of 4150 species and&#x2009;>&#x2009;1800 novel species but pointed at only 56 species that at least partially harbored pdu and cbi-cob-hem. While taxonomic diversity was highest in fecal samples of foregut-fermenting herbivores, higher pduC abundance and higher diversity of pdu/cbi-cob-hem related to higher potential for glycerol and 1,2-PD utilization of the less diverse microbiota of hindgut-fermenting carnivores in vitro.<br><br>CONCLUSION: Our approach combining metabolite and gene biomarker analysis with metagenomics and phenotypic characterization identified Pdu as a common function of fecal microbiota of captive wild animals shared by few taxa and stratified the potential of fecal microbiota for glycerol/1,2-PD utilization and cobalamin synthesis depending on diet and physiology of the host. This trait-based study suggests that the ability to utilize glycerol/1,2-PD is a key function of hindgut-fermenting carnivores, which does not relate to overall community diversity but links to the potential for cobalamin formation. Video Abstract.},
}
@article {pmid39300163,
year = {2024},
author = {Myeong, NR and Choe, YH and Shin, SC and Kim, J and Sul, WJ and Kim, M},
title = {Genomic profiling of Antarctic geothermal microbiomes using long-read, Hi-C, and single-cell techniques.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {1023},
pmid = {39300163},
issn = {2052-4463},
support = {PE24460//Korea Polar Research Institute (KOPRI)/ ; PE24070//Korea Polar Research Institute (KOPRI)/ ; PE24460//Korea Polar Research Institute (KOPRI)/ ; PE24460//Korea Polar Research Institute (KOPRI)/ ; Graduate Research Scholarship in 2017//Chung-Ang University (CAU)/ ; },
mesh = {Antarctic Regions ; *Microbiota ; *Single-Cell Analysis ; Hot Springs/microbiology ; Metagenomics ; Metagenome ; },
abstract = {Geothermal features in Antarctica provide favorable conditions for diverse microorganisms, yet their genomic diversity remains poorly understood. Here, we present an integrated dataset comprising PacBio HiFi and Hi-C metagenomic sequencing, along with single-cell amplified genomes (SAGs) from two high-altitude geothermal sites, Mount Melbourne and Mount Rittmann, in Antarctica. The long-read HiFi sequencing, coupled with Hi-C, enhances the understanding of microbiome diversity and functionality in this unique ecosystem by providing more complete and accurate genomic information. SAGs complement this by recovering rare microbial taxa and offering a strain-resolved perspective. This dataset aims to deepen our understanding of microbial evolution and ecology in Antarctic geothermal environments, and facilitate cross-comparison with other geothermal environments globally.},
}
@article {pmid39299940,
year = {2024},
author = {Obayori, OS and Salam, LB and Ashade, AO and Oseni, TD and Kalu, MD and Mustapha, FM},
title = {An animal charcoal contaminated cottage industry soil highlighted by halophilic archaea dominance and decimation of bacteria.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {40},
number = {10},
pages = {327},
pmid = {39299940},
issn = {1573-0972},
mesh = {*Metals, Heavy/analysis ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Archaea/classification/genetics/isolation &amp; purification/metabolism ; *Charcoal ; *Soil Pollutants/analysis ; *Soil/chemistry ; Nigeria ; High-Throughput Nucleotide Sequencing ; Animals ; Hydrocarbons/metabolism/analysis ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; },
abstract = {An animal charcoal contaminated cottage industry soil in Lagos, Nigeria (ACGT) was compared in an ex post facto study with a nearby unimpacted soil (ACGC). Hydrocarbon content was higher than regulatory limits in ACGT (180.2 mg/kg) but lower in ACGC (19.28 mg/kg). Heavy metals like nickel, cadmium, chromium and lead were below detection limit in ACGC. However, all these metals, except cadmium, were detected in ACGT, but at concentrations below regulatory limits. Furthermore, copper (253.205 mg/kg) and zinc (422.630 mg/kg) were above regulatory limits in ACGT. Next generation sequencing revealed that the procaryotic community was dominated by bacteria in ACGC (62%) while in ACGT archaea dominated (76%). Dominant phyla in ACGC were Euryarchaeota (37%), Pseudomonadota (16%) and Actinomycetota (12%). In ACGT it was Euryarchaeota (76%), Bacillota (9%), Pseudomonadota (7%) and Candidatus Nanohaloarchaeota (5%). Dominant Halobacteria genera in ACGT were Halobacterium (16%), Halorientalis (16%), unranked halophilic archaeon (13%) Salarchaeum (6%) and Candidatus Nanohalobium (5%), whereas ACGC showed greater diversity dominated by bacterial genera Salimicrobium (7%) and Halomonas (3%). Heavy metals homeostasis genes, especially for copper, were fairly represented in both soils but with bacterial taxonomic affiliations. Sites like ACGT, hitherto poorly studied and understood, could be sources of novel bioresources.},
}
@article {pmid39299726,
year = {2024},
author = {Zhou, H and Balint, D and Shi, Q and Vartanian, T and Kriegel, MA and Brito, I},
title = {Lupus and inflammatory bowel disease share a common set of microbiome features distinct from other autoimmune disorders.},
journal = {Annals of the rheumatic diseases},
volume = {},
number = {},
pages = {},
doi = {10.1136/ard-2024-225829},
pmid = {39299726},
issn = {1468-2060},
abstract = {OBJECTIVES: This study aims to elucidate the microbial signatures associated with autoimmune diseases, particularly systemic lupus erythematosus (SLE) and inflammatory bowel disease (IBD), compared with colorectal cancer (CRC), to identify unique biomarkers and shared microbial mechanisms that could inform specific treatment protocols.<br><br>METHODS: We analysed metagenomic datasets from patient cohorts with six autoimmune conditions-SLE, IBD, multiple sclerosis, myasthenia gravis, Graves' disease and ankylosing spondylitis-contrasting these with CRC metagenomes to delineate disease-specific microbial profiles. The study focused on identifying predictive biomarkers from species profiles and functional genes, integrating protein-protein interaction analyses to explore effector-like proteins and their targets in key signalling pathways.<br><br>RESULTS: Distinct microbial signatures were identified across autoimmune disorders, with notable overlaps between SLE and IBD, suggesting shared microbial underpinnings. Significant predictive biomarkers highlighted the diverse microbial influences across these conditions. Protein-protein interaction analyses revealed interactions targeting glucocorticoid signalling, antigen presentation and interleukin-12 signalling pathways, offering insights into possible common disease mechanisms. Experimental validation confirmed interactions between the host protein glucocorticoid receptor (NR3C1) and specific gut bacteria-derived proteins, which may have therapeutic implications for inflammatory disorders like SLE and IBD.<br><br>CONCLUSIONS: Our findings underscore the gut microbiome's critical role in autoimmune diseases, offering insights into shared and distinct microbial signatures. The study highlights the potential importance of microbial biomarkers in understanding disease mechanisms and guiding treatment strategies, paving the way for novel therapeutic approaches based on microbial profiles.<br><br>TRIAL REGISTRATION NUMBER: NCT02394964.},
}
@article {pmid39299446,
year = {2024},
author = {Wei, ZY and Feng, M and Zhang, DX and Jiang, CY and Deng, Y and Wang, ZJ and Feng, K and Song, Y and Zhou, N and Wang, YL and Liu, SJ},
title = {Deep insights into the assembly mechanisms, co-occurrence patterns, and functional roles of microbial community in wastewater treatment plants.},
journal = {Environmental research},
volume = {263},
number = {Pt 1},
pages = {120029},
doi = {10.1016/j.envres.2024.120029},
pmid = {39299446},
issn = {1096-0953},
abstract = {The understanding of activated sludge microbial status and roles is imperative for improving and enhancing the performance of wastewater treatment plants (WWTPs). In this study, we conducted a deep analysis of activated sludge microbial communities across five compartments (inflow, effluent, and aerobic, anoxic, anaerobic tanks) over temporal scales, employing high-throughput sequencing of 16S rRNA amplicons and metagenome data. Clearly discernible seasonal patterns, exhibiting cyclic variations, were observed in microbial diversity, assembly, co-occurrence network, and metabolic functions. Notably, summer samples exhibited higher α-diversity and were distinctly separated from winter samples. Our analysis revealed that microbial community assembly is influenced by both stochastic processes (66%) and deterministic processes (34%), with winter samples demonstrating more random assembly compared to summer. Co-occurrence patterns were predominantly mutualistic, with over 96% positive correlations, and summer networks were more organized than those in winter. These variations were significantly correlated with temperature, total phosphorus and sludge volume index. However, no significant differences were found among microbial community across five compartments in terms of β diversity. A core community of keystone taxa was identified, playing key roles in eight nitrogen and eleven phosphorus cycling pathways. Understanding the assembly mechanisms, co-occurrence patterns, and functional roles of microbial communities is essential for the design and optimization of biotechnological treatment processes in WWTPs.},
}
@article {pmid39299138,
year = {2024},
author = {Ren, WT and He, ZL and Lv, Y and Wang, HZ and Deng, L and Ye, SS and Du, JS and Wu, QL and Guo, WQ},
title = {Carbon chain elongation characterizations of electrode-biofilm microbes in electro-fermentation.},
journal = {Water research},
volume = {267},
number = {},
pages = {122417},
doi = {10.1016/j.watres.2024.122417},
pmid = {39299138},
issn = {1879-2448},
abstract = {The higher efficiency of electro-fermentation in synthesizing medium-chain fatty acids (MCFAs) compared to traditional fermentation has been acknowledged. However, the functional mechanisms of electrode-biofilm enhancing MCFAs synthesis remain research gaps. To address this, this study proposed a continuous flow electrode-biofilm reactor for chain elongation (CE). After 225 days of operation, stable electrode-biofilms formed and notably improved caproate yield by more than 38 %. The electrode-biofilm was enriched with more CE microorganisms and electroactive bacteria compared to the suspended sludge microorganisms, including Caproicibacterium, Oscillibacter and Pseudoramibacter. Besides, the upregulated CE pathways were evaluated by metagenomic analysis, and the results indicated that the pathways such as acetyl-CoA and malonyl-[acp] formation, reverse beta-oxidation, and fatty acid biosynthesis pathway were all markedly enhanced in cathodic biofilm, more than anodic biofilm and suspended microorganisms. Moreover, microbial community regulated processes like bacterial chemotaxis, flagellar assembly and quorum sensing, crucial for electrode-biofilm formation. Electron transfer, energy metabolism, and microbial interactions were found to be prominently upregulated in the cathodic biofilm, surpassing levels observed in anodic biofilm and suspended sludge microorganisms, which further enhanced CE efficiency. In addition, the statistical analyses further highlighted key microbial functions and interactions within the cathodic biofilm. Oscillospiraceae_bacterium was identified to be the most active microbe, alongside pivotal roles played by Caproiciproducens_sp._NJN-50, Clostridiales_bacterium, Prevotella_sp. and Pseudoclavibacter_caeni. Eventually, the proposed microbial collaboration mechanisms of cathodic biofilm were ascertained. Overall, this study uncovered the biological effects of the electrode-biofilm on MCFAs electrosynthesis, thereby advancing biochemicals production and filling the knowledge gaps in CE electroactive biofilm reactors.},
}
@article {pmid39298952,
year = {2024},
author = {Liu, J and Shi, J and Hu, Y and Su, Y and Zhang, Y and Wu, X},
title = {Flumethrin exposure perturbs gut microbiota structure and intestinal metabolism in honeybees (Apis mellifera).},
journal = {Journal of hazardous materials},
volume = {480},
number = {},
pages = {135886},
doi = {10.1016/j.jhazmat.2024.135886},
pmid = {39298952},
issn = {1873-3336},
abstract = {Flumethrin mitigates Varroa's harm to honeybee colonies; however, its residues in colonies threaten the fitness of honeybee hosts and gut microbiota. Our previous research has shown that flumethrin induces significant physiological effects on honeybee larvae; but the effects of flumethrin on the gut microbiota and metabolism of adult honeybees are still unknown. In this study, 1-day-old honeybees were exposed to 0, 0.01, 0.1, and 1 mg/L flumethrin for 14 days and the impacts of flumethrin on the intestinal system were evaluated. The results showed that exposure to 1 mg/L flumethrin significantly reduced honeybee survival and the activities of antioxidative enzymes (superoxide dismutase and catalase) and detoxification enzymes (glutathione S-transferase) in honeybee heads. Moreover, exposure to 0.01, 0.1, and 1 mg/L flumethrin significantly decreased the diversity of the honeybee gut microbiota. Results from untargeted metabolomics showed that long-term exposure to 0.01, 0.1, and 1 mg/L flumethrin caused changes in the metabolic pathways of honeybee gut microbes. Furthermore, increased metabolism of phenylalanine, tyrosine, and tryptophan derivatives was observed in honeybee gut microbes. These findings underscore the importance of careful consideration in using pesticides in apiculture and provide a basis for safeguarding honeybees from pollutants, considering the effects on gut microbes.},
}
@article {pmid39298898,
year = {2024},
author = {Seller-Brison, C and Brison, A and Yu, Y and Robinson, SL and Fenner, K},
title = {Adaptation towards catabolic biodegradation of trace organic contaminants in activated sludge.},
journal = {Water research},
volume = {266},
number = {},
pages = {122431},
doi = {10.1016/j.watres.2024.122431},
pmid = {39298898},
issn = {1879-2448},
abstract = {Trace organic contaminants (TrOCs) are omnipresent in wastewater treatment plants (WWTPs), yet, their removal during wastewater treatment is oftentimes incomplete and underlying biotransformation mechanisms are not fully understood. In this study, we elucidate how different factors, including pre-exposure levels and duration, influence microbial adaptation towards catabolic TrOC biodegradation and its potential role in biological wastewater treatment. Four sequencing batch reactors (SBRs) were operated in parallel in three succeeding phases, adding and removing a selection of 26 TrOCs at different concentration levels. After each phase of SBR operation, a series of batch experiments was conducted to monitor biotransformation kinetics of those same TrOCs across various spike concentrations. For half of our test TrOCs, we detected increased biotransformation in sludge pre-exposed to TrOC concentrations ≥5 µg L[-1] over a 30-day period, with most significant differences observed for the insect repellent DEET and the artificial sweetener saccharin. Accordingly, 16S rRNA amplicon sequencing revealed enrichment of taxa that have previously been linked to catabolic biodegradation of several test TrOCs, e.g., Bosea sp. and Shinella sp. for acesulfame degradation, and Pseudomonas sp. for caffeine, cyclamate, DEET, metformin, paracetamol, and isoproturon degradation. We further conducted shotgun metagenomics to query for gene products previously reported to be involved in the TrOCs' biodegradation pathways. In the future, directed microbial adaptation may be a solution to improve bioremediation of TrOCs in contaminated environments or in WWTPs.},
}
@article {pmid39298897,
year = {2024},
author = {Wang, N and Li, S and Shi, M and Ni, N and Zhang, X and Guo, X and Lin, H and Luo, Y},
title = {Trajectory of antibiotic resistome response to antibiotics gradients: A comparative study from pharmaceutical and associated wastewater treatment plants to receiving river.},
journal = {Water research},
volume = {266},
number = {},
pages = {122444},
doi = {10.1016/j.watres.2024.122444},
pmid = {39298897},
issn = {1879-2448},
abstract = {Pharmaceutical wastewater often contains significant levels of antibiotic residues, which continuously induce and promote antibiotic resistance during the sewage treatment process. However, the specific impact of antibiotics on the emergence of antibiotic resistance genes (ARGs), microbiomes, and mobile genetic elements (MGEs), as well as the dose-response relationship remain unclear. Herein, through metagenomic sequencing and analysis, we investigated the fate, transmission, and associated risk of ARGs over a ten-year period of exposure to a gradient of sulfonamide antibiotics at a pharmaceutical wastewater treatment plant (PWWTP), an associated wastewater treatment plant (WWTP), and the receiving river. Through abundance comparison and principal co-ordinates analysis (PCoA), our results revealed distinct ARG, microbiome, and MGE profiles across different antibiotic concentrations. Notably, there was a decreasing trend in the abundance of ARGs and MGEs as the antibiotic concentrations were attenuated (p < 0.05). Further partial least squares path modeling analysis, Procrustes analysis and network analysis indicated that variation in MGEs and microbiomes were the driving forces behind the distribution of ARGs. Based on these findings, we proposed an antibiotic-microbiome-MGE-ARG dissemination paradigm, in which integrons as key drivers were closely associated with prevalent ARGs such as sul1, sul2, and aadA. With a focus on human pathogenic bacteria and the associated health risks of ARGs, we conducted pathogen source analysis and calculated the antibiotic resistome risk index (ARRI). Our findings highlighted potential risks associated with the transition from PWWTP to WWTP, raising concerns regarding risk amplification due to the mixed treatment of antibiotic-laden industrial wastewater and domestic sewage. Overall, the results of our study provide valuable information for optimizing wastewater treatment practices to better manage antibiotic resistance.},
}
@article {pmid39298862,
year = {2024},
author = {Karadayı, S and Yılmaz, &#x130; and Özbek, T and Karadayı, B},
title = {Transfer and persistence of microbiota markers from the human hand to the knife: A preliminary study.},
journal = {Journal of forensic and legal medicine},
volume = {107},
number = {},
pages = {102757},
doi = {10.1016/j.jflm.2024.102757},
pmid = {39298862},
issn = {1878-7487},
abstract = {New scientific techniques and methods are always needed to link the perpetrators to the incident or the crime scene. Recent microbiota studies based on NGS (Next-generation sequencing) show that various biological samples from crime scenes have the potential to be used in forensic investigations. Especially when DNA traces belonging to more than one person are insufficient to fully determine the genetic profile, a secret sample, such as a microbiota sample created by the suspect's touch, can be used. In this preliminary study, a fictionalized experimental model was designed to investigate the transfer and persistence of the hand microbiome on the knife handle, which has a high potential to be used in criminal incidents, by metagenomic analysis methods. In addition, it was aimed to determine the transfer of specific bacterial species identified only to the person among the five participants onto the knife handle and their persistence over time. In the first stage of the research, samples were collected from the hands of 5 volunteer participants using the swap method, including their palms. Then, after each participant held a different knife, samples were collected from the knife handles via swabs from different angles of the knives at 4 and 24 h and analyzed by metagenomic methods. The findings of this preliminary study showed that the heatmap graphs generated after UniFrac distance analysis were not successful in establishing any similarity between the hand samples and the post-transfer knife handle samples. Nonetheless, it was observed that the transfer of bacterial species detected in the hand samples to knives differed according to the individuals and some bacterial species were transferred to the knife samples held by the participants. The number of bacterial species detected that are specific to each participant's hand sample was 302 in total, and it was determined that a total of 8.28 % of these bacterial species were transferred to the knife handle samples of the 4th hour and 6.95 % to the knife samples of the 24th hour. In the presented study, considering the transfer of some bacterial species in the hand microbiome, which are effective in the variation between individuals, onto the knife; It has been evaluated that some rare bacterial species can be important potential markers to associate the object with the perpetrator.},
}
@article {pmid39298515,
year = {2024},
author = {Kandathil, AJ and Blair, PW and Lu, J and Anantharam, R and Kobba, K and Robinson, ML and Alharthi, S and Ndawula, EC and Dumler, JS and Kakooza, F and Lamorde, M and Thomas, DL and Salzberg, SL and Manabe, YC},
title = {Metagenomic next generation sequencing of plasma RNA for diagnosis of unexplained, acute febrile illness in Uganda.},
journal = {PLoS neglected tropical diseases},
volume = {18},
number = {9},
pages = {e0012451},
doi = {10.1371/journal.pntd.0012451},
pmid = {39298515},
issn = {1935-2735},
abstract = {Metagenomic next generation metagenomic sequencing (mNGS) has proven to be a useful tool in the diagnosis and identification of novel human pathogens and pathogens not identified on routine clinical microbiologic tests. In this study, we applied mNGS to characterize plasma RNA isolated from 42 study participants with unexplained acute febrile illness (AFI) admitted to tertiary referral hospitals in Mubende and Arua, Uganda. Study participants were selected based on clinical criteria suggestive of viral infection (i.e., thrombocytopenia, leukopenia). The study population had a median age of 28 years (IQR:24 to 38.5) and median platelet count of 114 x103 cells/mm3 (IQR:66,500 to 189,800). An average of 25 million 100 bp reads were generated per sample. We identified strong signals from diverse virus, bacteria, fungi, or parasites in 10 (23.8%) of the study participants. These included well recognized pathogens like Helicobacter pylori, human herpes virus-8, Plasmodium falciparum, Neisseria gonorrhoeae, and Rickettsia conorii. We further confirmed Rickettsia conorii infection, the cause of Mediterranean Spotted Fever (MSF), using PCR assays and Sanger sequencing. mNGS was a useful addition for detection of otherwise undetected pathogens and well-recognized non-pathogens. This is the first report to describe the molecular confirmation of a hospitalized case of MSF in sub-Saharan Africa (SSA). Further studies are needed to determine the utility of mNGS for disease surveillance in similar settings.},
}
@article {pmid39298488,
year = {2024},
author = {Worthan, SB and McCarthy, RDP and Delaleau, M and Stikeleather, R and Bratton, BP and Boudvillain, M and Behringer, MG},
title = {Evolution of pH-sensitive transcription termination in Escherichia coli during adaptation to repeated long-term starvation.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {39},
pages = {e2405546121},
doi = {10.1073/pnas.2405546121},
pmid = {39298488},
issn = {1091-6490},
support = {W911NF-21-1-0161//DOD | USA | AFC | CCDC | ARO | Life Sciences Division, Army Research Office (Life Sciences Division ARO)/ ; R35GM150625//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; ANR-19-CE44-0009-01//Agence Nationale de la Recherche (ANR)/ ; },
mesh = {*Escherichia coli/genetics/metabolism ; Hydrogen-Ion Concentration ; *Escherichia coli Proteins/genetics/metabolism ; Adaptation, Physiological/genetics ; Mutation ; Transcription Termination, Genetic ; Gene Expression Regulation, Bacterial ; Rho Factor/metabolism/genetics ; Evolution, Molecular ; },
abstract = {Fluctuating environments that consist of regular cycles of co-occurring stress are a common challenge faced by cellular populations. For a population to thrive in constantly changing conditions, an ability to coordinate a rapid cellular response is essential. Here, we identify a mutation conferring an arginine-to-histidine (Arg to His) substitution in the transcription terminator Rho. The rho R109H mutation frequently arose in Escherichia coli populations experimentally evolved under repeated long-term starvation conditions, during which the accumulation of metabolic waste followed by transfer into fresh media results in drastic environmental pH fluctuations associated with feast and famine. Metagenomic sequencing revealed that populations containing the rho mutation also possess putative loss-of-function mutations in ydcI, which encodes a recently characterized transcription factor associated with pH homeostasis. Genetic reconstructions of these mutations show that the rho allele confers plasticity via an alkaline-induced reduction of Rho function that, when found in tandem with a ΔydcI allele, leads to intracellular alkalization and genetic assimilation of Rho mutant function. We further identify Arg to His substitutions at analogous sites in rho alleles from species that regularly experience neutral to alkaline pH fluctuations in their environments. Our results suggest that Arg to His substitutions in Rho may serve to rapidly coordinate complex physiological responses through pH sensing and shed light on how cellular populations use environmental cues to coordinate rapid responses to complex, fluctuating environments.},
}
@article {pmid39298196,
year = {2024},
author = {Barber, DG and Davies, CA and Hartley, IP and Tennant, RK},
title = {Evaluation of commercial RNA extraction kits for long-read metatranscriptomics in soil.},
journal = {Microbial genomics},
volume = {10},
number = {9},
pages = {},
pmid = {39298196},
issn = {2057-5858},
mesh = {*Soil Microbiology ; Microbiota/genetics ; Soil/chemistry ; Transcriptome ; Gene Expression Profiling/methods ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, RNA/methods ; RNA/genetics/isolation &amp; purification ; RNA, Bacterial/genetics/isolation &amp; purification ; },
abstract = {Metatranscriptomic analysis of the soil microbiome has the potential to reveal molecular mechanisms that drive soil processes regulated by the microbial community. Therefore, RNA samples must be of sufficient yield and quality to robustly quantify differential gene expression. While short-read sequencing technology is often favoured for metatranscriptomics, long-read sequencing has the potential to provide several benefits over short-read technologies. The ability to resolve complete transcripts on a portable sequencing platform for a relatively low capital expenditure makes Oxford Nanopore Technology an attractive prospect for addressing many of the challenges of soil metatranscriptomics. To fully enable long-read metatranscriptomic analysis of the functional molecular pathways expressed in these diverse habitats, RNA purification methods from soil must be optimised for long-read sequencing. Here we compare RNA samples purified using five commercially available extraction kits designed for use with soil. We found that the Qiagen RNeasy PowerSoil Total RNA Kit performed the best across RNA yield, quality and purity and was robust across different soil types. We found that sufficient sequencing depth can be achieved to characterise the active community for total RNA samples using Oxford Nanopore Technology, and discuss its current limitations for differential gene expression analysis in soil studies.},
}
@article {pmid39298479,
year = {2024},
author = {Hellewell, J and Horsfield, ST and von Wachsmann, J and Gurbich, TA and Finn, RD and Iqbal, Z and Roberts, LW and Lees, JA},
title = {CELEBRIMBOR: Core and accessory genes from metagenomes.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btae542},
pmid = {39298479},
issn = {1367-4811},
abstract = {MOTIVATION: Metagenome-Assembled Genomes (MAGs) or Single-cell Amplified Genomes (SAGs) are often incomplete, with sequences missing due to errors in assembly or low coverage. This presents a particular challenge for the identification of true gene frequencies within a microbial population, as core genes missing in only a few assemblies will be mischaracterized by current pangenome approaches.<br><br>RESULTS: Here, we present CELEBRIMBOR, a Snakemake pangenome analysis pipeline which uses a measure of genome completeness to automatically adjust the frequency threshold at which core genes are identified, enabling accurate core gene identification in MAGs and SAGs.<br><br>AVAILABILITY: CELEBRIMBOR is published under open source Apache 2.0 licence at https://github.com/bacpop/CELEBRIMBOR and is available as a Docker container from this repository. Supplementary material is available in the online version of the article.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}
@article {pmid39297677,
year = {2024},
author = {Bulka, O and Edwards, E},
title = {Metagenome from ACT-3/CF: an anaerobic chloroform-degrading microbial community.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0067424},
doi = {10.1128/mra.00674-24},
pmid = {39297677},
issn = {2576-098X},
abstract = {Here, we present the metagenome of an anaerobic chloroform respiring mixed microbial community used for bioremediation. Our objective was to obtain draft genomes of key microorganisms in the culture.},
}
@article {pmid39296299,
year = {2024},
author = {Wang, X and Li, H and Yang, Y and Wu, Z and Wang, Z and Li, D and Xia, W and Zou, S and Liu, Y and Wang, F},
title = {Geographic and environmental impacts on gut microbiome in Himalayan langurs (Semnopithecus schistaceus) and Xizang macaques (Macaca mulatta vestita).},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1452101},
pmid = {39296299},
issn = {1664-302X},
abstract = {INTRODUCTION: Gut microbiome plays a crucial role in the health of wild animals. Their structural and functional properties not only reflect the host's dietary habits and habitat conditions but also provide essential support for ecological adaptation in various environments.<br><br>METHODS: This study investigated the gut microbiome of Himalayan langurs (Semnopithecus schistaceus) and Xizang macaques (Macaca mulatta vestita) across different geographic regions using 16S rRNA gene and metagenomic sequencing.<br><br>RESULTS: Results showed distinct clustering patterns in gut microbiota based on geographic location. Soil had an insignificant impact on host gut microbiome. Himalayan langurs from mid-altitude regions exhibited higher levels of antibiotic resistance genes associated with multidrug resistance, while Xizang macaques from high-altitude regions showed a broader range of resistance genes. Variations in carbohydrate-active enzymes and KEGG pathways indicated unique metabolic adaptations to different environments.<br><br>DISCUSSION: These findings provide valuable insights into the health and conservation of these primates and the broader implications of microbial ecology and functional adaptations in extreme conditions.},
}
@article {pmid39295709,
year = {2024},
author = {Mariam, S and Kshirsagar, R and Hasan, S and Khadtare, Y and Rajpurohit, KS and Rai, H and Newaskar, D and Deo, P},
title = {Implant Mechanics, Biological Milieu, and Peri-Implantitis: A Narrative Review.},
journal = {Cureus},
volume = {16},
number = {8},
pages = {e67173},
pmid = {39295709},
issn = {2168-8184},
abstract = {Dental implants constitute an important treatment modality for rehabilitating edentulous and partially edentulous arches. With more implant systems in the market, understanding the mechanical aspects of implants is crucial in understanding this indispensable therapy. However, microflora-related factors i.e. biological factors are also crucial. Despite the tremendous success rate of dental implants, it is not averse to failure. Both mechanical and microbial aspects in seclusion or together predispose to implant failure. Newer technological advances have paved the way for advanced techniques to identify the not-so-common flora causing implant failure. This review focuses on detailed mechanical and biological aspects and the sealing agent used to seal the implant-abutment interface. It also focuses on advanced molecular techniques like metagenomics and transcriptomics. A thorough literature search was performed with selected articles from electronic databases. A combination of in-vivo and in-vitro studies were considered to provide comprehensive information on the subject. Both the biomechanical aspects like micro gap, and microleakage, as well as microbial movements play confluent roles in implant failure. The focus should be on the different aspects through which microflora can penetrate the inner parts of the implant. Also, newer culture-independent techniques of detecting previously undetected oral flora should be included in future studies.},
}
@article {pmid39294762,
year = {2024},
author = {Cruz-Cano, R and Kolb, M and Saldaña-Vázquez, RA and Bretón-Deval, L and Cruz-Cano, N and Aldama-Cervantes, A},
title = {Existing evidence on the use of environmental DNA as an operational method for studying rivers: a systematic map and thematic synthesis.},
journal = {Environmental evidence},
volume = {13},
number = {1},
pages = {2},
pmid = {39294762},
issn = {2047-2382},
support = {IN211921//UNAM-PAPIIT/ ; CVU: 516486//CONACYT/ ; },
abstract = {BACKGROUND: Environmental DNA (eDNA) is the DNA that can be extracted from an environmental sample, enabling the monitoring of whole biological communities across a large number of samples, at a potentially lower cost, which can significantly benefit river conservation. A systematic mapping protocol was designed to investigate the use of eDNA in rivers, specifically in terms of research topics, geographic and taxonomic biases, as well as information gaps. Furthermore, the potential research opportunities of eDNA in rivers and possible paths to find this kind of information on available platforms are identified.<br><br>METHODS: A published systematic map protocol was applied, consisting of a search for published articles and gray literature in two bibliographic databases and one search engine. All search results were submitted to a 2-stage screening for relevance and pertinence in accordance with pre-defined eligibility criteria. Data extraction and codification regarding country of study, year, taxonomic group, sequencing platform, and type of technique employed resulted in a publicly available database.<br><br>RESULTS: From 7372 studies initially obtained by the search, 545 met the inclusion criteria spanning a period from 2003 to 2022. The five countries with most studies are: USA (134), Japan (61), China (54), Brazil (29) and the UK (25). The most used fragments to analyze DNA are 16S and COI, whilst 26S and 23S are the least used. Only 84 (15%) of the studies reported hypervariable regions, among which the most used are V4 and V5. Regarding taxonomic groups, fishes are most often studied (176), followed by bacteria (138) and virus (52), while fungi is the least studied group (3). Concerning data availability, 229 (42%) studies provided access to sequencing data.<br><br>CONCLUSIONS: This study presents a comprehensive analysis of the available evidence regarding the implementation of the eDNA methods in rivers. The findings indicate that since the year 2003, this approach has been applied to aquatic lotic systems, and their recent increase can be attributed to the development of Next-Generation-Sequencing technologies and their reduced costs. However, there is a bias towards high-income countries, particularly USA and Europe. Widespread use and applications of this approach at a global level would allow for the generation of a large amount of information that can be compared between countries to understand if responses of aquatic systems follow similar patterns worldwide.},
}
@article {pmid39294752,
year = {2024},
author = {Góngora, E and Lirette, AO and Freyria, NJ and Greer, CW and Whyte, LG},
title = {Metagenomic survey reveals hydrocarbon biodegradation potential of Canadian high Arctic beaches.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {72},
pmid = {39294752},
issn = {2524-6372},
support = {Multi-Partner Research Initiative//Fisheries and Oceans Canada/ ; 273122//Fonds de recherche du Qu&#xe9;bec - Nature et technologies/ ; Polar Continental Shelf Project//Natural Resources Canada/ ; Northern Scientific Training Program//Polar Knowledge Canada/ ; },
abstract = {BACKGROUND: Decreasing sea ice coverage across the Arctic Ocean due to climate change is expected to increase shipping activity through previously inaccessible shipping routes, including the Northwest Passage (NWP). Changing weather conditions typically encountered in the Arctic will still pose a risk for ships which could lead to an accident and the uncontrolled release of hydrocarbons onto NWP shorelines. We performed a metagenomic survey to characterize the microbial communities of various NWP shorelines and to determine whether there is a metabolic potential for hydrocarbon degradation in these microbiomes.<br><br>RESULTS: We observed taxonomic and functional gene evidence supporting the potential of NWP beach microbes to degrade various types of hydrocarbons. The metagenomic and metagenome-assembled genome (MAG) taxonomy showed that known hydrocarbon-degrading taxa are present in these beaches. Additionally, we detected the presence of biomarker genes of aerobic and anaerobic degradation pathways of alkane and aromatic hydrocarbons along with complete degradation pathways for aerobic alkane degradation. Alkane degradation genes were present in all samples and were also more abundant (33.8&#x2009;&#xb1;&#x2009;34.5 hits per million genes, HPM) than their aromatic hydrocarbon counterparts (11.7&#x2009;&#xb1;&#x2009;12.3&#xa0;HPM). Due to the ubiquity of MAGs from the genus Rhodococcus (23.8% of the MAGs), we compared our MAGs with Rhodococcus genomes from NWP isolates obtained using hydrocarbons as the carbon source to corroborate our results and to develop a pangenome of Arctic Rhodococcus. Our analysis revealed that the biodegradation of alkanes is part of the core pangenome of this genus. We also detected nitrogen and sulfur pathways as additional energy sources and electron donors as well as carbon pathways providing alternative carbon sources. These pathways occur in the absence of hydrocarbons allowing microbes to survive in these nutrient-poor beaches.<br><br>CONCLUSIONS: Our metagenomic analyses detected the genetic potential for hydrocarbon biodegradation in these NWP shoreline microbiomes. Alkane metabolism was the most prevalent type of hydrocarbon degradation observed in these tidal beach ecosystems. Our results indicate that bioremediation could be used as a cleanup strategy, but the addition of adequate amounts of N and P fertilizers, should be considered to help bacteria overcome the oligotrophic nature of NWP shorelines.},
}
@article {pmid39294577,
year = {2024},
author = {He, S and Liu, H and Hu, X and Zhao, J and Liang, J and Zhang, X and Chen, J and Zeng, H and Sun, G},
title = {Exploring the clinical and diagnostic value of metagenomic next-generation sequencing for urinary tract infection: a systematic review and meta-analysis.},
journal = {BMC infectious diseases},
volume = {24},
number = {1},
pages = {1000},
pmid = {39294577},
issn = {1471-2334},
mesh = {*Urinary Tract Infections/diagnosis/microbiology ; Humans ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; Sensitivity and Specificity ; ROC Curve ; },
abstract = {BACKGROUND: A new pathogen detection tool, metagenomic next-generation sequencing (mNGS), has been widely used for infection diagnosis, but the clinical and diagnostic value of mNGS in urinary tract infection (UTI) remains inconclusive. This systematic review with meta-analysis aimed to investigate the efficacy of mNGS in treating UTIs.<br><br>METHODS: A comprehensive literature search was performed in PubMed, Web of Science, Embase, and the Cochrane Library, and eligible studies were selected based on the predetermined criteria. The quality of the included studies was assessed via the Quality Assessment of Diagnostic Accuracy Studies-2 (QUADAS-2) tool, and the certainty of evidence (CoE) was measured by the Grading of Recommendations, Assessment, Development, and Evaluations (GRADE) score. Then, the positive detection rate (PDR), pooled sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR), diagnostic odds ratio (DOR), and area under the curve of the summary receiver operating characteristic curve (AUROC) was estimated in Review Manager, Stata, and MetaDisc. Subgroup analysis, meta-regression, and sensitivity analysis were performed to reveal the potential factors that influence internal heterogeneity.<br><br>RESULTS: A total of 17 studies were selected for further analysis. The PDR of mNGS was markedly greater than that of culture (odds ratio (OR)&#x2009;=&#x2009;2.87, 95% confidence interval [CI]: 1.72-4.81, p&#x2009;<&#x2009;0.001, I[2]&#x2009;=&#x2009;90%). The GRADE score presented a very low CoE. Then, the pooled sensitivity was 0.89 (95% CI: 0.86-0.91, I[2]&#x2009;=&#x2009;39.65%, p&#x2009;=&#x2009;0.06), and the pooled specificity was 0.75 (95% CI: 0.51-0.90, I[2]&#x2009;=&#x2009;88.64%, p&#x2009;<&#x2009;0.001). The AUROC of the studies analyzed was 0.89 (95% CI: 0.86-0.92). The GRADE score indicated a low CoE.<br><br>CONCLUSION: The current evidence shows that mNGS has favorable diagnostic performance for UTIs. More high-quality prospective randomized controlled trials (RCTs) are expected to verify these findings and provide more information about mNGS in UTI treatment and prognosis.},
}
@article {pmid39294312,
year = {2024},
author = {Li, D and Wang, Y and Li, X and Zhang, Z and Wang, G and Zhang, Y and Chen, L},
title = {Exploring microbial diversity and function in companion planting systems of white clover and orchard grass.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {21609},
pmid = {39294312},
issn = {2045-2322},
support = {32172769//National Natural Science Foundation of China/ ; },
mesh = {*Trifolium/microbiology/genetics/growth &amp; development ; *Soil Microbiology ; *Rhizosphere ; *Microbiota/genetics ; Dactylis/genetics/microbiology ; Metagenomics/methods ; Bacteria/genetics/classification ; Biodiversity ; },
abstract = {Companion planting of white clover (Trifolium repens L.) with orchard grass (Dactylis glomerata L.), a famous hay grass, improves the forage quality of orchard grass. Microbiome profiling techniques can reveal the specific role of white clover companion planting with orchard grass. This study aimed to explore the microbiome distribution and gene functions of rhizosphere and non-rhizosphere soil via companion planting systems of white clover and orchard grass. From metagenomics sequencing analysis, we confirmed the significant role of white clover on soil environment modeling during companion planting with orchard grass. Twenty-eight biomarkers of rhizosphere soil organisms were identified during companion planting, including Proteobacteria, Betaproteobacteria, Flavobacteriia, and Caulobacterales. The number of gene functions of nitrogen and carbon fixation in companion planting was higher than that in single plants, indicating new functional flora for companion planting. We characterized specific rhizosphere effects, typical biomarker flora, and potential regulatory mechanisms for white clover-related companion planting by metagenomics analyses.},
}
@article {pmid39294129,
year = {2024},
author = {Bozzi, D and Neuenschwander, S and Cruz Dávalos, DI and Sousa da Mota, B and Schroeder, H and Moreno-Mayar, JV and Allentoft, ME and Malaspinas, AS},
title = {Towards predicting the geographical origin of ancient samples with metagenomic data.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {21794},
pmid = {39294129},
issn = {2045-2322},
mesh = {Humans ; *DNA, Ancient/analysis ; *Metagenomics/methods ; *Metagenome ; Geography ; Microbiota/genetics ; },
abstract = {Reconstructing the history-such as the place of birth and death-of an individual sample is a fundamental goal in ancient DNA (aDNA) studies. However, knowing the place of death can be particularly challenging when samples come from museum collections with incomplete or erroneous archives. While analyses of human DNA and isotope data can inform us about the ancestry of an individual and provide clues about where the person lived, they cannot specifically trace the place of death. Moreover, while ancient human DNA can be retrieved, a large fraction of the sequenced molecules in ancient DNA studies derive from exogenous DNA. This DNA-which is usually discarded in aDNA analyses-is constituted mostly by microbial DNA from soil-dwelling microorganisms that have colonized the buried remains post-mortem. In this study, we hypothesize that remains of individuals buried in the same or close geographic areas, exposed to similar microbial communities, could harbor more similar metagenomes. We propose to use metagenomic data from ancient samples' shotgun sequencing to locate the place of death of a given individual which can also help to solve cases of sample mislabeling. We used a k-mer-based approach to compute similarity scores between metagenomic samples from different locations and propose a method based on dimensionality reduction and logistic regression to assign a geographical origin to target samples. We apply our method to several public datasets and observe that individual samples from closer geographic locations tend to show higher similarities in their metagenomes compared to those of different origin, allowing good geographical predictions of test samples. Moreover, we observe that the genus Streptomyces commonly infiltrates ancient remains and represents a valuable biomarker to trace the samples' geographic origin. Our results provide a proof of concept and show how metagenomic data can also be used to shed light on the place of origin of ancient samples.},
}
@article {pmid39293811,
year = {2024},
author = {Liu, Y and Ong, SL and Gedye, K and Truglio, M and Prabakar, S},
title = {Behind the Scenes: Metagenomic Analysis of Bacterial Communities in Sustainable Depilation of Sheepskin.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxae244},
pmid = {39293811},
issn = {1365-2672},
abstract = {AIMS: The leather industry is embracing eco-friendly technologies for both regulatory compliance and sustainable growth. While enzymatic depilation provides a greener alternative to traditional beamhouse methods, its complexity often leads to higher costs. To address this, we examined the performance of sheepskins' native bacterial flora in acetic acid conditions with low environmental impact.<br><br>METHODS AND RESULTS: Utilizing metagenomic techniques, we analyzed the bacterial community dynamics during the depilation process. This investigation revealed a notable increase in microbial diversity and richness in acetic acid treatments compared to water treatments. At the class level, a post-processing decrease in Gammaproteobacteria dominance was observed, while Actinomycetia numbers surged in the acetic acid group. In contrast, the water group showed an increase in Bacteroidia. Order-level analysis indicated reductions in Pseudomonadales and increases in Actinomycetales with acetic acid treatment, whereas Flavobacteriales was more prevalent in water-treated liquors. At the family level, Moraxellaceae decreased and Micrococcaceae increased in the acetic acid group, in contrast to the marked rise of Weeksellaceae in the water group. Temporal analyses further highlighted the evolving bacterial landscapes under different treatments. Moreover, acetic acid treatment fostered a stable microbial community, beneficial for sustainable leather processing. Functional pathways were predicted using PICRUSt2. It showed that significantly enriched degradation pathways in the water group were less abundant in the acetic acid group, potentially preventing substrate matrix damage during depilation.<br><br>CONCLUSIONS: The study underscores the transformative potential of acetic acid for the leather industry, offering a pathway to reduce pollution while maintaining economic viability. By enhancing our understanding of microbial interactions during depilation, this study opens avenues for refining these eco-friendly techniques. Our findings advocate for a shift towards greener depilation methods and contribute to the broader dialogue on sustainable manufacturing practices, emphasizing the importance of leveraging indigenous microbial communities for environmental and economic gains.},
}
@article {pmid39293760,
year = {2024},
author = {Chen, L and Zhang, P and Li, Y and Liang, J and Zhang, G},
title = {Genome-centric metagenomic analysis reveals mechanisms of quorum sensing promoting anaerobic digestion under sulfide stress: Syntrophic metabolism and microbial self-adaptation.},
journal = {The Science of the total environment},
volume = {954},
number = {},
pages = {176240},
doi = {10.1016/j.scitotenv.2024.176240},
pmid = {39293760},
issn = {1879-1026},
abstract = {Sulfide stress is a common inhibition factor in anaerobic digestion systems with sulfur-rich feedstocks. Quorum sensing (QS) signaling molecule N-acyl-homoserine lactones (AHLs) possess positive effect on promoting anaerobic digestion. However, the micro-biological mechanisms of AHLs affecting syntrophic metabolism and microbial self-adaptation have not yet been deciphered in anaerobic digestion under sulfide stress. In this study, the CH4 production increased by 21.34 % at 20 μM AHLs addition in anaerobic digestion under sulfide stress. AHLs contributed to establishing potential syntrophic relationship between acidifying bacteria (unclassified_o__Bacteroidales, Lentimicrobium, Acetoanaerobium, Longilinea, and Sphaerochaetaa) and Methanothrix. AHLs promoted syntrophic metabolism by boosting microbial metabolic activity and interspecies electron transfer (IET) process under sulfide stress. For microbial metabolic activity, AHLs promoted the key enzyme synthesis in acidogenesis and methanogenesis. For IET process, AHLs promoted the assembly and synthesis of conductive pili, and synthesis and secretion of riboflavin. Furthermore, AHLs promoted microbial self-adaptation including two component system, lipopolysaccharide biosynthesis, and DNA repair, which were important evidences that microbial resistance to sulfide stress was enhanced by AHLs. Microbial self-adaptation provided favorable foundation and safeguard for syntrophic metabolisms under sulfide stress. These findings deciphered the micro-biological mechanisms of AHLs enhancing anaerobic digestion under sulfide stress.},
}
@article {pmid39293510,
year = {2024},
author = {Zhang, T and Li, H and Jiang, M and Hou, H and Gao, Y and Li, Y and Wang, F and Wang, J and Peng, K and Liu, YX},
title = {Nanopore sequencing: flourishing in its teenage years.},
journal = {Journal of genetics and genomics = Yi chuan xue bao},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgg.2024.09.007},
pmid = {39293510},
issn = {1673-8527},
abstract = {Over the past decade, nanopore sequencing has experienced significant advancements and changes, transitioning from an initially emerging technology to a significant instrument in the field of genomic sequencing. However, as advancements in next-generation sequencing technology persist, nanopore sequencing also improves. This paper reviews the developments, applications, and outlook on nanopore sequencing technology. Currently, nanopore sequencing supports both DNA and RNA sequencing, making it widely applicable in areas such as telomere-to-telomere (T2T) genome assembly, direct RNA sequencing (DRS), and metagenomics. The openness and versatility of nanopore sequencing have established it as a preferred option for an increasing number of research teams, signaling a transformative influence on life science research. As nanopore sequencing technology advances, it provides a faster, more cost-effective approach with extended read lengths, demonstrating the significant potential for complex genome assembly, pathogen detection, environmental monitoring, and human disease research, offering a fresh perspective in sequencing technologies.},
}
@article {pmid39293343,
year = {2024},
author = {Mao, TQ and Zhang, Y and Ou, YF and Li, XF and Zheng, YL and Liang, X and Liu, M and Hou, LJ and Dong, HP},
title = {Temperature differentially regulates estuarine microbial N2O production along a salinity gradient.},
journal = {Water research},
volume = {267},
number = {},
pages = {122454},
doi = {10.1016/j.watres.2024.122454},
pmid = {39293343},
issn = {1879-2448},
abstract = {Nitrous oxide (N2O) is atmospheric trace gas that contributes to climate change and affects stratospheric and ground-level ozone concentrations. Ammonia oxidizers and denitrifiers contribute to N2O emissions in estuarine waters. However, as an important climate factor, how temperature regulates microbial N2O production in estuarine water remains unclear. Here, we have employed stable isotope labeling techniques to demonstrate that the N2O production in estuarine waters exhibited differential thermal response patterns between nearshore and offshore regions. The optimal temperatures (Topt) for N2O production rates (N2OR) were higher at nearshore than offshore sites. [15]N-labeled nitrite ([15]NO2[-]) experiments revealed that at the nearshore sites dominated by ammonia-oxidizing bacteria (AOB), the thermal tolerance of [15]N-N2OR increases with increasing salinity, suggesting that N2O production by AOB-driven nitrifier denitrification may be co-regulated by temperature and salinity. Metatranscriptomic and metagenomic analyses of enriched water samples revealed that the denitrification pathway of AOB is the primary source of N2O, while clade II N2O-reducers dominated N2O consumption. Temperature regulated the expression patterns of nitrite reductase (nirK) and nitrous oxide reductase (nosZ) genes from different sources, thereby influencing N2O emissions in the system. Our findings contribute to understanding the sources of N2O in estuarine waters and their response to global warming.},
}
@article {pmid39293338,
year = {2024},
author = {Bakir-Gungor, B and Temiz, M and Inal, Y and Cicekyurt, E and Yousef, M},
title = {CCPred: Global and population-specific colorectal cancer prediction and metagenomic biomarker identification at different molecular levels using machine learning techniques.},
journal = {Computers in biology and medicine},
volume = {182},
number = {},
pages = {109098},
doi = {10.1016/j.compbiomed.2024.109098},
pmid = {39293338},
issn = {1879-0534},
abstract = {Colorectal cancer (CRC) ranks as the third most common cancer globally and the second leading cause of cancer-related deaths. Recent research highlights the pivotal role of the gut microbiota in CRC development and progression. Understanding the complex interplay between disease development and metagenomic data is essential for CRC diagnosis and treatment. Current computational models employ machine learning to identify metagenomic biomarkers associated with CRC, yet there is a need to improve their accuracy through a holistic biological knowledge perspective. This study aims to evaluate CRC-associated metagenomic data at species, enzymes, and pathway levels via conducting global and population-specific analyses. These analyses utilize relative abundance values from human gut microbiome sequencing data and robust classification models are built for disease prediction and biomarker identification. For global CRC prediction and biomarker identification, the features that are identified by SelectKBest (SKB), Information Gain (IG), and Extreme Gradient Boosting (XGBoost) methods are combined. Population-based analysis includes within-population, leave-one-dataset-out (LODO) and cross-population approaches. Four classification algorithms are employed for CRC classification. Random Forest achieved an AUC of 0.83 for species data, 0.78 for enzyme data and 0.76 for pathway data globally. On the global scale, potential taxonomic biomarkers include ruthenibacterium lactatiformanas; enzyme biomarkers include RNA 2' 3' cyclic 3' phosphodiesterase; and pathway biomarkers include pyruvate fermentation to acetone pathway. This study underscores the potential of machine learning models trained on metagenomic data for improved disease prediction and biomarker discovery. The proposed model and associated files are available at https://github.com/TemizMus/CCPRED.},
}
@article {pmid39288738,
year = {2024},
author = {Cai, P and Korem, T},
title = {Microsynteny is a powerful front for microbial strain tracking.},
journal = {Cell reports methods},
volume = {4},
number = {9},
pages = {100862},
doi = {10.1016/j.crmeth.2024.100862},
pmid = {39288738},
issn = {2667-2375},
mesh = {*Metagenomics/methods ; Bacteria/genetics/classification ; Software ; },
abstract = {Genomic diversity within species can be driven by both point mutations and larger structural variations, but so far, strain-tracking approaches have focused mostly on the former. In a recent issue of Nature Biotechnology, Ley and colleagues[1] introduce SynTracker, a tool designed for scalable strain tracking with microsynteny in low-coverage metagenomic settings.},
}
@article {pmid39293053,
year = {2024},
author = {Quarton, S and Livesey, A and Jeff, C and Hatton, C and Scott, A and Parekh, D and Thickett, D and McNally, A and Sapey, E},
title = {Metagenomics in the Diagnosis of Pneumonia: Protocol for a Systematic Review.},
journal = {JMIR research protocols},
volume = {13},
number = {},
pages = {e57334},
doi = {10.2196/57334},
pmid = {39293053},
issn = {1929-0748},
mesh = {Humans ; *Metagenomics/methods ; *Pneumonia/diagnosis/microbiology ; Systematic Reviews as Topic ; High-Throughput Nucleotide Sequencing/methods ; Pneumonia, Ventilator-Associated/diagnosis/microbiology ; Bronchoalveolar Lavage Fluid/microbiology ; },
abstract = {BACKGROUND: Causative pathogens are currently identified in only a minority of pneumonia cases, which affects antimicrobial stewardship. Metagenomic next-generation sequencing (mNGS) has potential to enhance pathogen detection due to its sensitivity and broad applicability. However, while studies have shown improved sensitivity compared with conventional microbiological methods for pneumonia diagnosis, it remains unclear whether this can translate into clinical benefit. Most existing studies focus on patients who are ventilated, readily allowing for analysis of bronchoalveolar lavage fluid (BALF). The impact of sample type on the use of metagenomic analysis remains poorly defined. Similarly, previous studies rarely differentiate between the types of pneumonia involved-community-acquired pneumonia (CAP), hospital-acquired pneumonia (HAP), or ventilator-associated pneumonia (VAP)-which have different clinical profiles.<br><br>OBJECTIVE: This study aims to determine the clinical use of mNGS in CAP, HAP, and VAP, compared with traditional microbiological methods.<br><br>METHODS: We aim to review all studies (excluding case reports of a series of fewer than 10 people) of adult patients with suspected or confirmed pneumonia that compare metagenomic analysis with traditional microbiology techniques, including culture, antigen-based testing, and polymerase chain reaction-based assays. Relevant studies will be identified through systematic searches of the Embase, MEDLINE, Scopus, and Cochrane CENTRAL databases. Screening of titles, abstracts, and subsequent review of eligible full texts will be done by 2 separate reviewers (SQ and 1 of AL, CJ, or CH), with a third clinician (ES) providing adjudication in case of disagreement. Our focus is on the clinical use of metagenomics for patients with CAP, HAP, and VAP. Data extracted will focus on clinically important outcomes-pathogen positivity rate, laboratory turnaround time, impact on clinical decision-making, length of stay, and 30-day mortality. Subgroup analyses will be performed based on the type of pneumonia (CAP, HAP, or VAP) and sample type used. The risk of bias will be assessed using the QUADAS-2 tool for diagnostic accuracy studies. Outcome data will be combined in a random-effects meta-analysis, and where this is not possible, a narrative synthesis will be undertaken.<br><br>RESULTS: The searches were completed with the assistance of a medical librarian on January 13, 2024, returning 5750 records. Screening and data extraction are anticipated to be completed by September 2024.<br><br>CONCLUSIONS: Despite significant promise, the impact of metagenomic analysis on clinical pathways remains unclear. Furthermore, it is unclear whether the use of this technique will alter depending on whether the pneumonia is a CAP, HAP, or VAP or the sample type that is collected. This systematic review will assess the current evidence base to support the benefit of clinical outcomes for metagenomic analysis, depending on the setting of pneumonia diagnosis or specimen type used. It will identify areas where further research is needed to advance this methodology into routine care.<br><br>TRIAL REGISTRATION: PROSPERO CRD42023488096; https://tinyurl.com/3suy7cma.<br><br>DERR1-10.2196/57334.},
}
@article {pmid39292721,
year = {2024},
author = {Bastien, GE and Cable, RN and Batterbee, C and Wing, AJ and Zaman, L and Duhaime, MB},
title = {Virus-host interactions predictor (VHIP): Machine learning approach to resolve microbial virus-host interaction networks.},
journal = {PLoS computational biology},
volume = {20},
number = {9},
pages = {e1011649},
doi = {10.1371/journal.pcbi.1011649},
pmid = {39292721},
issn = {1553-7358},
abstract = {Viruses of microbes are ubiquitous biological entities that reprogram their hosts' metabolisms during infection in order to produce viral progeny, impacting the ecology and evolution of microbiomes with broad implications for human and environmental health. Advances in genome sequencing have led to the discovery of millions of novel viruses and an appreciation for the great diversity of viruses on Earth. Yet, with knowledge of only "who is there?" we fall short in our ability to infer the impacts of viruses on microbes at population, community, and ecosystem-scales. To do this, we need a more explicit understanding "who do they infect?" Here, we developed a novel machine learning model (ML), Virus-Host Interaction Predictor (VHIP), to predict virus-host interactions (infection/non-infection) from input virus and host genomes. This ML model was trained and tested on a high-value manually curated set of 8849 virus-host pairs and their corresponding sequence data. The resulting dataset, 'Virus Host Range network' (VHRnet), is core to VHIP functionality. Each data point that underlies the VHIP training and testing represents a lab-tested virus-host pair in VHRnet, from which meaningful signals of viral adaptation to host were computed from genomic sequences. VHIP departs from existing virus-host prediction models in its ability to predict multiple interactions rather than predicting a single most likely host or host clade. As a result, VHIP is able to infer the complexity of virus-host networks in natural systems. VHIP has an 87.8% accuracy rate at predicting interactions between virus-host pairs at the species level and can be applied to novel viral and host population genomes reconstructed from metagenomic datasets.},
}
@article {pmid39292303,
year = {2024},
author = {Singh, K and Malla, MA and Kumar, A and Yadav, S},
title = {Biological monitoring of soil pollution caused by two different zinc species using earthworms.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {39292303},
issn = {1614-7499},
abstract = {Zinc oxide nanoparticles (ZnO-NPs) are commonly used in both commercial and agricultural sectors. As a result, ZnO-NPs are extensively discharged into soil ecosystems, creating a significant environmental issue. Therefore, it is crucial to assess their influence on the soil ecology to ensure its secure and enduring utilization in the future. The exact degree of toxicity associated with ZnO-NPs and their ionic form is still uncertain. To address the challenges, the study used the soil bioindicator earthworm species Eudrilus eugeniae as an experimental model to evaluate the effects of two zinc species (ZnO-NPs and ZnCl2) at 100, 250, 500, and 750 mg kg[-1] and control (0 mg kg[-1]) in garden soil over 28 days. The investigation also examined the impact of exposure on survival, reproduction, neuro-biomarker, avoidance behavior, and accumulation. The highest avoidance rates were 27.5% for ZnO-NP and 37.5% for ZnCl2 at 750 mg kg[-1]. ZnCl2 treatment reduced juvenile production by 3.73 ± 1.73, while ZnO-NPs showed 4.67 ± 1.15. At 750 mg kg[-1], soils with ZnCl2 (63.3%) demonstrated lower survival rates than those with ZnO-NPs (53.3%), likely because of higher Zn ion levels. After 28 days of exposure, ZnCl2 (536.32 ± 11 mol min[-1]) activated AChE enzymes more than ZnO-NPs (497.7 ± 59 mol min[-1]) at the same dose, compared to control (145.88 ± 28 to 149.41 ± 23 mol min[-1]). Nanoparticles and zinc ions bioaccumulated and reacted negatively with the neurotoxic marker AChE, affecting earthworm reproduction and behavior. However, earthworms exposed to ZnCl2 exhibited less intestinal Zn than those exposed to NPs. The present work contradicts the finding that ZnO-NPs have hazardous effects on soil organisms. The results indicate that earthworm E. eugeniae may significantly affect soil metal uptake from metallic nanoparticles (NPs). This may help design NP soil pollution mitigation strategies. The study offers valuable information for establishing a relationship between the environmental toxicity of ZnO-NPs and soil ecosystems.},
}
@article {pmid39290858,
year = {2024},
author = {Zhou, G and Li, J and Liang, X and Yang, B and He, X and Tang, H and Guo, H and Liu, G and Cui, W and Chen, Y and Yang, Y},
title = {Multi-omics revealed the mechanism of feed efficiency in sheep by the combined action of the host and rumen microbiota.},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {18},
number = {},
pages = {367-379},
pmid = {39290858},
issn = {2405-6383},
abstract = {This study was conducted to investigate potential regulatory mechanisms of feed efficiency (FE) in sheep by linking rumen microbiota with its host by the multi-omics analysis. One hundred and ninety-eight hybrid female sheep (initial body weight = 30.88 ± 4.57 kg; 4-month-old) were selected as candidate sheep. Each test sheep was fed in an individual pen for 60 days, and the residual feed intake (RFI) was calculated. The ten candidate sheep with the highest RFI were divided into the Low-FE group, and the ten with the lowest RFI were divided into the High-FE group, all selected for sample collection. The RFI, average daily gain and average daily feed intake were highly significantly different between the two experimental groups (P < 0.05). Compared with Low-FE group, the insulin-like growth factor-1 and very low-density lipoprotein in serum and the propionate in rumen significantly increased in High-FE group (P < 0.01), but the acetate:propionate ratio in rumen significantly decreased in High-FE group (P = 0.034). Metagenomics revealed Selenomonas ruminantium, Selenomonas sp. and Faecalibacterium prausnitzi i were key bacteria, and increased abundance of the genes encoding the enzymes for cellulose degradation and production of propionate in High-FE group. The results of proteomics and section showed the rumen papilla length (P < 0.001) and expression of carbonic anhydrase and Na[+]/K[+]-ATPase were significantly higher in High-FE group (P < 0.05). On the other hand, the acetyl-CoA content significantly increased in the liver of High-FE group (P = 0.002). The relative expression levels of insulin-like growth factor-1 and apolipoprotein A4 genes were significantly up-regulated in the liver of High-FE group (P < 0.01), but relative expression level of monoacylglycerol O-acyltransferase 3 gene was significantly down-regulated (P = 0.037). These findings provide the mechanism by which the collaborative interaction between rumen microbiota fermentation and host uptake and metabolism of fermentation products impacts feed efficiency traits in sheep.},
}
@article {pmid39290728,
year = {2024},
author = {Scholpp, AC and Schilbert, HM and Viehöver, P and Weisshaar, B and Beckstette, M and Neumann, JM and Bednarz, H and Niehaus, K},
title = {Differential gene expression in leaves and roots of Hydrangea serrata treated with aluminium chloride.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1412189},
pmid = {39290728},
issn = {1664-462X},
abstract = {Hydrangea serrata, also knowen as the Japanese tea hortensia, is known for its sweet taste and health properties of bevarages produced from this plant. The H. serrata 3,4-dihydroisocoumarins, hydrangenol and phyllodulcin harbour a variety of biological activities and pharmacological properties. Therefore, a detailed understanding of dihydroisocoumarin biosynthesis in H. serrata is of major interest. Their biosynthesis is assumed to be enhanced by elicitors and mediated by polyketide synthases like in cases of phenylpropanoid derived phytoalexins. A de-novo transcriptome assembly of leaves and roots from the aluminium chloride treatment group versus the control group alongside with annotation was generated. Secondary plant metabolites were analysed by LC-MS. It revealed that a terpene synthase and a triterpenoid synthase gene as well as lignin biosynthesis encoding genes were upregulated in roots. Many genes for transporters, glycosyl, and other transferases as well as glycosylases were found to be differentially expressed in both organs. As no differentially expressed polyketide synthase gene homolog was found, the relative leaf and root 3,4-dihydroisocoumarin content was analysed by LC-MS measurement. Although Hydrangea species are known for their aluminium detoxification using phenylpropanoid-derived compounds, the levels of 3,4- dihydroisocoumarins were not enhanced. In this metabolite analysis, an organ- specific accumulation profile of hydrangenol, phyllodulcin, hydrangeic acid and their mono- and di-glycosides was figured out.},
}
@article {pmid39290662,
year = {2024},
author = {Thormar, EA and Hansen, SB and Jørgensen, LVG and Limborg, MT},
title = {Sampling fish gut microbiota - A genome-resolved metagenomic approach.},
journal = {Ecology and evolution},
volume = {14},
number = {9},
pages = {e70302},
pmid = {39290662},
issn = {2045-7758},
abstract = {Despite a surge in microbiota-focused studies in teleosts, few have reported functional data on whole metagenomes as it has proven difficult to extract high biomass microbial DNA from fish intestinal samples. The zebrafish is a promising model organism in functional microbiota research, yet studies on the functional landscape of the zebrafish gut microbiota through shotgun based metagenomics remain scarce. Thus, a consensus on an appropriate sampling method accurately representing the zebrafish gut microbiota, or any fish species is lacking. Addressing this, we systematically tested four methods of sampling the zebrafish gut microbiota: collection of faeces from the tank, the whole gut, intestinal content, and the application of ventral pressure to facilitate extrusion of gut material. Additionally, we included water samples as an environmental control to address the potential influence of the environmental microbiota on each sample type. To compare these sampling methods, we employed a combination of genome-resolved metagenomics and 16S metabarcoding techniques. We observed differences among sample types on all levels including sampling, bioinformatic processing, metagenome co-assemblies, generation of metagenome-assembled genomes (MAGs), functional potential, MAG coverage, and population level microdiversity. Comparison to the environmental control highlighted the potential impact of the environmental contamination on data interpretation. While all sample types tested are informative about the zebrafish gut microbiota, the results show that optimal sample type for studying fish microbiomes depends on the specific objectives of the study, and here we provide a guide on what factors to consider for designing functional metagenome-based studies on teleost microbiomes.},
}
@article {pmid39289490,
year = {2024},
author = {Bai, B and Tuerxun, G and Tuerdi, A and Maimaiti, R and Sun, Y and Abudukerimu, A},
title = {Analysis of vaginal flora diversity and study on the role of Porphyromonas asaccharolytica in promoting IL-1β in regulating cervical cancer.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {21731},
pmid = {39289490},
issn = {2045-2322},
support = {2022D01C185//Natural Science Foundation of the Xinjiang Uygur Autonomous Region/ ; },
mesh = {Female ; Humans ; *Uterine Cervical Neoplasms/microbiology/virology/pathology/genetics ; *Vagina/microbiology ; *Porphyromonas/genetics/isolation &amp; purification ; *Interleukin-1beta/genetics/metabolism ; *Microbiota/genetics ; Adult ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Papillomavirus Infections/virology/microbiology/complications ; },
abstract = {Cervical cancer, a prevalent malignancy in the female reproductive tract, exhibits a high incidence. Existing evidence indicates a robust correlation between alterations in vaginal flora composition and the progression of cervical cancer. Nevertheless, there is a lack of clarity concerning the specific microorganisms within the vaginal microbiota that are linked to the onset and development of cervical cancer, as well as the mechanisms through which they exert carcinogenic effects. The 16 S ribosomal (rRNA) and metagenomic sequencing technology were used to analyze vaginal microorganisms, and screening for human papillomavirus (HPV) positive cervical cancer-associated microbial markers using fold change in mean bacterial abundance. Moreover, vaginal microenvironmental factors were detected, and the local vaginal inflammatory state in patients with cervical cancer was subjected to assay via qRT-PCR and ELISA. The hub inflammatory genes were screened by transcriptome sequencing after co-culture of bacteria and normal cervical epithelial cells, and an in vitro model was utilized to assess the impacts of inflammatory factors on cervical cancer. Both cervical cancer patients and HPV-positive patients showed significant changes in the composition of the vaginal flora, characterised by a decrease in the abundance of Lactobacillus and an increase in the abundance of a variety of anaerobic bacteria; The microbial sequencing identified Porphyromonas, Porphyromonas_asaccharolytica, and Porphyromonas_uenonis as microbial markers for HPV-associated cervical cancer. Vaginal inflammatory factors in patients with cervical cancer were overexpressed. After Porphyromonas_asaccharolytica intervention on cervical epithelial H8 cells, interleukin (IL)-1β, a hub differential gene, markedly promoted tumor-associated biological behaviors at the in vitro cytological level in cervical cancer. This study for the first demonstrated that Porphyromonas, Porphyromonas_asaccharolytica, and Porphyromonas_uenonis could serve as novel microbial markers for cervical cancer. Moreover, Porphyromonas_asaccharolytica was identified as having the ability to induce the overexpression of inflammatory genes in cervical epithelial cells to create a favorable microenvironment for the onset and development of cervical cancer. The effects of dysbacteriosis on cervical cancer were microbiologically elucidated.},
}
@article {pmid39289365,
year = {2024},
author = {Peng, X and Wang, S and Wang, M and Feng, K and He, Q and Yang, X and Hou, W and Li, F and Zhao, Y and Hu, B and Zou, X and Deng, Y},
title = {Metabolic interdependencies in thermophilic communities are revealed using co-occurrence and complementarity networks.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {8166},
pmid = {39289365},
issn = {2041-1723},
mesh = {*Metabolic Networks and Pathways/genetics ; *Archaea/genetics/metabolism ; *Bacteria/metabolism/genetics/classification ; *Metagenome/genetics ; *Microbiota ; Hot Springs/microbiology ; Phylogeny ; Microbial Interactions ; Hot Temperature ; },
abstract = {Microbial communities exhibit intricate interactions underpinned by metabolic dependencies. To elucidate these dependencies, we present a workflow utilizing random matrix theory on metagenome-assembled genomes to construct co-occurrence and metabolic complementarity networks. We apply this approach to a temperature gradient hot spring, unraveling the interplay between thermal stress and metabolic cooperation. Our analysis reveals an increase in the frequency of metabolic interactions with rising temperatures. Amino acids, coenzyme A derivatives, and carbohydrates emerge as key exchange metabolites, forming the foundation for syntrophic dependencies, in which commensalistic interactions take a greater proportion than mutualistic ones. These metabolic exchanges are most prevalent between phylogenetically distant species, especially archaea-bacteria collaborations, as a crucial adaptation to harsh environments. Furthermore, we identify a significant positive correlation between basal metabolite exchange and genome size disparity, potentially signifying a means for streamlined genomes to leverage cooperation with metabolically richer partners. This phenomenon is also confirmed by another composting system which has a similar wide range of temperature fluctuations. Our workflow provides a feasible way to decipher the metabolic complementarity mechanisms underlying microbial interactions, and our findings suggested environmental stress regulates the cooperative strategies of thermophiles, while these dependencies have been potentially hardwired into their genomes during co-evolutions.},
}
@article {pmid39288877,
year = {2024},
author = {Wang, X and Zhang, Y and Zhou, H and Wu, M and Shan, J and Yan, X},
title = {Investigating drivers of N2 loss and N2O reducers in paddy soils across China.},
journal = {The Science of the total environment},
volume = {954},
number = {},
pages = {176287},
doi = {10.1016/j.scitotenv.2024.176287},
pmid = {39288877},
issn = {1879-1026},
abstract = {Denitrification plays a pivotal role in nitrogen (N) cycling in rice paddies, significantly impacting N loss and greenhouse gas emissions. Accurate quantification of net N2 emissions from paddy fields is therefore essential for improving fertilizer N use efficiency. However, challenges in directly measuring gaseous N2 hinder our understanding of microbially-mediated N loss in paddy soils at large scales. In this study, we investigated net N2 loss and its influencing factors in 45 paddy soils across China using membrane inlet mass spectrometry and N2/Ar technique, complemented by microbial community analysis via metagenomics. Potential N2 loss rates varied from 0.41 to 3.58 nmol N g[-1] h[-1], with no significant regional differences. However, soils from rice-upland rotation (1.72 ± 0.64 nmol N g[-1] h[-1]) and mono-rice cropping systems (1.41 ± 0.53 nmol N g[-1] h[-1]) exhibited higher N2 loss rates compared to double-rice cropping soils (1.13 ± 0.62 nmol N g[-1] h[-1]). Our results revealed a unimodal relationship between soil N2 loss rates and soil pH, with N2O reducers and soil properties primarily regulating regional variations in N2 loss. Significant ecological differentiation was observed within both nosZ Clade I and Clade II, with soil pH emerging as the key factor shaping their community composition. Specifically, in rice-upland rotations, soil moisture and pH significantly influenced nosZ Clade I, while in double-rice cropping systems, soil texture and pH were the main factors affecting nosZ Clade II, thereby driving N2 loss. These findings enhance our understanding of N2 loss dynamics in paddy soil ecosystems, underscoring the critical role of N2O reducers on microbial-derived N2 loss and highlighting the importance of developing strategies to mitigate N2O emissions by balancing N2 loss through the manipulation of N2O-reducing and N2O-producing microbes.},
}
@article {pmid39288380,
year = {2024},
author = {Ye, LY and Zhao, XL and Qin, JJ and Lin, J},
title = {Metagenomic next-generation sequencing assisted in the successful treatment of pneumonia caused by Talaromyces marneffei in an immunocompetent patient.},
journal = {Journal of infection in developing countries},
volume = {18},
number = {8},
pages = {1296-1300},
doi = {10.3855/jidc.19061},
pmid = {39288380},
issn = {1972-2680},
mesh = {Humans ; *Talaromyces/genetics/isolation &amp; purification ; Male ; *High-Throughput Nucleotide Sequencing ; Middle Aged ; *Metagenomics/methods ; *Voriconazole/therapeutic use ; *Antifungal Agents/therapeutic use ; Pneumonia/microbiology/drug therapy ; Mycoses/microbiology/drug therapy/diagnosis ; Treatment Outcome ; Immunocompetence ; },
abstract = {INTRODUCTION: Talaromyces marneffei (T. marneffei), a kind of endemic opportunistic pathogen, was previously thought to occur in HIV-positive individuals and non-HIV hosts with impaired immune function. However, the infection of T. marneffei in patient with normal immune function was rarely reported.<br><br>CASE PRESENTATION: We report a case of severe pneumonia caused by T. marneffei in an immunocompetent and HIV-negative patient, which was rapidly confirmed by metagenomics next-generation sequencing (mNGS) and treated successfully. The patient was a previously healthy 63-year-old male, who was admitted to hospital with fever for 11 days, cough and sputum for 1 week, and chest distress for 4 days. The infection of T. marneffei was quickly determined by alveolar lavage under bedside bronchoscope and mNGS test.<br><br>RESULTS: Patient's condition improved rapidly after voriconazole treatment, and he was evaluated as a HIV-negative case of T. marneffei infection with normal immune function. This is a sporadic case of T. marneffei in non-endemic areas, and mNGS played a very important role in the treatment of the disease. The patient's immune function was relatively normal which was rare in clinical practice.},
}
@article {pmid39287428,
year = {2024},
author = {Andreani-Gerard, CM and Cambiazo, V and González, M},
title = {Biosynthetic gene clusters from uncultivated soil bacteria of the Atacama Desert.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0019224},
doi = {10.1128/msphere.00192-24},
pmid = {39287428},
issn = {2379-5042},
abstract = {Soil microorganisms mediate several biological processes through the secretion of natural products synthesized in specialized metabolic pathways, yet functional characterization in ecological contexts remains challenging. Using culture-independent metagenomic analyses of microbial DNA derived directly from soil samples, we examined the potential of biosynthetic gene clusters (BGCs) from six bacterial communities distributed along an altitudinal gradient of the Andes Mountains in the Atacama Desert. We mined 38 metagenome-assembled genomes (MAGs) and identified 168 BGCs. Results indicated that most predicted BGCs were classified as non-ribosomal-peptides (NRP), post-translational modified peptides (RiPP), and terpenes, which were mainly identified in genomes of species from Acidobacteriota and Proteobacteria phyla. Based on BGC composition according to types of core biosynthetic genes, six clusters of MAGs were observed, three of them with predominance for a single phylum, of which two also showed specificity to a single sampling site. Comparative analyses of accessory genes in BGCs showed associations between membrane transporters and other protein domains involved in specialized metabolism with classes of biosynthetic cores, such as resistance-nodulation-cell division (RND) multidrug efflux pumps with RiPPs and the iron-dependent transporter TonB with terpenes. Our findings increase knowledge regarding the biosynthetic potential of uncultured bacteria inhabiting pristine locations from one of the oldest and driest nonpolar deserts on Earth.IMPORTANCEMuch of what we know about specialized metabolites in the Atacama Desert, including Andean ecosystems, comes from isolated microorganisms intended for drug development and natural product discovery. To complement research on the metabolic potential of microbes in extreme environments, comparative analyses on functional annotations of biosynthetic gene clusters (BGCs) from uncultivated bacterial genomes were carried out. Results indicated that in general, BGCs encode for structurally unique metabolites and that metagenome-assembled genomes did not show an obvious relationship between the composition of their core biosynthetic potential and taxonomy or geographic distribution. Nevertheless, some members of Acidobacteriota showed a phylogenetic relationship with specific metabolic traits and a few members of Proteobacteria and Desulfobacterota exhibited niche adaptations. Our results emphasize that studying specialized metabolism in environmental samples may significantly contribute to the elucidation of structures, activities, and ecological roles of microbial molecules.},
}
@article {pmid39287376,
year = {2024},
author = {Bucher-Johannessen, C and Senthakumaran, T and Avershina, E and Birkeland, E and Hoff, G and Bemanian, V and Tunsjø, H and Rounge, TB},
title = {Species-level verification of Phascolarctobacterium association with colorectal cancer.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0073424},
doi = {10.1128/msystems.00734-24},
pmid = {39287376},
issn = {2379-5077},
abstract = {We have previously demonstrated an association between increased abundance of Phascolarctobacterium and colorectal cancer (CRC) and adenomas in two independent Norwegian cohorts. Here we seek to verify our previous findings using new cohorts and methods. In addition, we characterize lifestyle and sex specificity, the functional potential of the Phascolarctobacterium species, and their interaction with other microbial species. We analyze Phascolarctobacterium with 16S rRNA sequencing, shotgun metagenome sequencing, and species-specific qPCR, using 2350 samples from three Norwegian cohorts-CRCAhus, NORCCAP, and CRCbiome-and a large publicly available data set, curatedMetagenomicData. Using metagenome-assembled genomes from the CRCbiome study, we explore the genomic characteristics and functional potential of the Phascolarctobacterium pangenome. Three species of Phascolarctobacterium associated with adenoma/CRC were consistently detected by qPCR and sequencing. Positive associations with adenomas/CRC were verified for Phascolarctobacterium succinatutens and negative associations were shown for Phascolarctobacterium faecium and adenoma in curatedMetagenomicData. Men show a higher prevalence of P. succinatutens across cohorts. Co-occurrence among Phascolarctobacterium species was low (<6%). Each of the three species shows distinct microbial composition and forms distinct correlation networks with other bacterial taxa, although Dialister invisus was negatively correlated to all investigated Phascolarctobacterium species. Pangenome analyses showed P. succinatutens to be enriched for genes related to porphyrin metabolism and degradation of complex carbohydrates, whereas glycoside hydrolase enzyme 3 was specific to P. faecium.IMPORTANCEUntil now Phascolarctobacterium has been going under the radar as a CRC-associated genus despite having been noted, but overseen, as such for over a decade. We found not just one, but two species of Phascolarctobacterium to be associated with CRC-Phascolarctobacterium succinatutens was more abundant in adenoma/CRC, while Phascolarctobacterium faecium was less abundant in adenoma. Each of them represents distinct communities, constituted by specific microbial partners and metabolic capacities-and they rarely occur together in the same patients. We have verified that P. succinatutens is increased in adenoma and CRC and this species should be recognized among the most important CRC-associated bacteria.},
}
@article {pmid39287374,
year = {2024},
author = {Vinogradova, E and Mukhanbetzhanov, N and Nurgaziyev, M and Jarmukhanov, Z and Aipova, R and Sailybayeva, A and Bekbossynova, M and Kozhakhmetov, S and Kushugulova, A},
title = {Impact of urbanization on gut microbiome mosaics across geographic and dietary contexts.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0058524},
doi = {10.1128/msystems.00585-24},
pmid = {39287374},
issn = {2379-5077},
abstract = {UNLABELLED: This study provides a comprehensive assessment of how urban-rural divides influence gut microbial diversity and composition across the distinct geographical landscapes of Kazakhstan, elucidating the intricate interplay between lifestyle, environment, and gut microbiome. In this prospective cohort study, we enrolled 651 participants from urban centers and rural settlements across Kazakhstan, following ethical approval and informed consent. Comprehensive demographic, dietary, and stool sample data were collected. 16S rRNA gene sequencing and shotgun metagenomics techniques were employed to delineate the intricate patterns of the gut microbiome. A rigorous statistical framework dissected the interplay between urbanization gradients, geography, dietary lifestyles, and microbial dynamics. Our findings demonstrate a stark microbial divide between urban and rural gut ecosystems. The study found significant differences in gut microbiome diversity and composition between urban and rural populations in Kazakhstan. Urban microbiomes exhibited reduced diversity, higher Firmicutes/Bacteroidetes ratios, and increased prevalence of genera Coprococcus and Parasutterella. In contrast, rural populations had greater microbial diversity and abundance of Ligilactobacillus, Sutterella, and Paraprevotella. Urbanization also influenced dietary patterns, with urban areas consuming more salt, cholesterol, and protein, while rural areas had diets richer in carbohydrates and fiber. The study also identified distinct patterns in the prevalence of antibiotic resistance genes and virulence factors between urban and rural gut microbiomes. This study sheds light on how urbanization may be deeply involved in shaping the intricate mosaic of the gut microbiome across Kazakhstan's diverse geographical and dietary landscapes, underscoring the complex interplay between environmental exposures, dietary lifestyles, and the microbial residents inhabiting our intestines.<br><br>IMPORTANCE: The study examined gut microbiome composition across diverse geographical locations in Kazakhstan, spanning urban centers and rural settlements. This allows for thoroughly investigating how urbanization gradients and geographic factors shape the gut microbiome. The study's examination of the gut resistome and prevalence of virulence-associated genes provide essential insights into the public health implications of urbanization-driven microbiome alterations. Collecting comprehensive demographic, dietary, and stool sample data enables the researchers to better understand the relationships between urbanization, nutritional patterns, and gut microbiome composition. The findings have important implications for understanding how urbanization-driven microbiome changes may impact human health and well-being, paving the way for tailored interventions to restore a balanced gut microbial ecology.},
}
@article {pmid39287279,
year = {2024},
author = {Xing, W and Yu, J and Cui, S and Liu, L and Zhi, Y and Zhang, T and Zhou, J},
title = {Analysis of the correlation between gut microbiome imbalance and the development of endometrial cancer based on metagenomics.},
journal = {Medicine},
volume = {103},
number = {37},
pages = {e39596},
pmid = {39287279},
issn = {1536-5964},
mesh = {Humans ; Female ; *Endometrial Neoplasms/microbiology/genetics ; *Gastrointestinal Microbiome/genetics ; Case-Control Studies ; Middle Aged ; Prospective Studies ; *Metagenomics/methods ; Aged ; Adult ; },
abstract = {Endometrial cancer (EC) is the most prevalent gynecologic malignancy, with a higher risk in obese women, suggesting the potential involvement of gut microbiota in the progression of EC. However, there is no direct evidence of a connection between EC and the human gut microbiota. Using metagenomic sequencing, we investigated the relationship between gut microbiome imbalance and cancer development in patients with EC. In this prospective case-control study, we included 15 patients with EC based on endometrial biopsy in the case group and 15 women admitted to the hospital for female pelvic floor issues during the same time who did not have endometrial lesions from January 2023 to June 2023 in control group. The microbiota structure of EC cases and controls without benign or malignant endometrial lesions during the same time period was analyzed using metagenomic sequencing technology. We employed Alpha diversity analysis to reflect the richness and diversity of microbial communities. Statistical algorithm Bray-Curtis was utilized to calculate pairwise distances between samples, obtaining a beta diversity distance matrix. Subsequently, hierarchical clustering analysis was conducted based on the distance matrix. The results showed that the composition of bacterial colonies in both groups was dominated by Firmicutes, which had a higher proportion in the control group, followed by Bacteroidetes in the control group and Proteobacteria and Bacteroidetes in the case group. The abundance of Klebsiella (P = .02) was significantly higher, and the abundance of Alistipes (P = .04), Anearobutyricum (P = .01), and bacteria in Firmicutes such as Oscillospira and Catenibacterium was markedly lower in the case group than in the control group. These results demonstrated conclusively that a gut microbiome imbalance was associated with the development of EC.},
}
@article {pmid39287139,
year = {2024},
author = {Pu, L and Shamir, R},
title = {4CAC: 4-class classifier of metagenome contigs using machine learning and assembly graphs.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkae799},
pmid = {39287139},
issn = {1362-4962},
support = {1339/18//Israel Science Foundation/ ; //Edmond J. Safra Center for Bioinformatics at Tel-Aviv University/ ; //Planning &amp; Budgeting Committee/ ; //Council for Higher Education/ ; },
abstract = {Microbial communities usually harbor a mix of bacteria, archaea, plasmids, viruses and microeukaryotes. Within these communities, viruses, plasmids, and microeukaryotes coexist in relatively low abundance, yet they engage in intricate interactions with bacteria. Moreover, viruses and plasmids, as mobile genetic elements, play important roles in horizontal gene transfer and the development of antibiotic resistance within microbial populations. However, due to the difficulty of identifying viruses, plasmids, and microeukaryotes in microbial communities, our understanding of these minor classes lags behind that of bacteria and archaea. Recently, several classifiers have been developed to separate one or more minor classes from bacteria and archaea in metagenome assemblies. However, these classifiers often overlook the issue of class imbalance, leading to low precision in identifying the minor classes. Here, we developed a classifier called 4CAC that is able to identify viruses, plasmids, microeukaryotes, and prokaryotes simultaneously from metagenome assemblies. 4CAC generates an initial four-way classification using several sequence length-adjusted XGBoost models and further improves the classification using the assembly graph. Evaluation on simulated and real metagenome datasets demonstrates that 4CAC substantially outperforms existing classifiers and combinations thereof on short reads. On long reads, it also shows an advantage unless the abundance of the minor classes is very low. 4CAC runs 1-2 orders of magnitude faster than the other classifiers. The 4CAC software is available at https://github.com/Shamir-Lab/4CAC.},
}
@article {pmid39287136,
year = {2024},
author = {Pérot, P and Tondeur, L and Moutailler, S and Chrétien, D and Corre-Catelin, N and Vayssier-Taussat, M and Eloit, M and Chirouze, C and Cazorla, C and , },
title = {Broad range molecular detection methods identify only Borrelia spp. in erythema migrans biopsies and blood of tick-bitten patients.},
journal = {One health (Amsterdam, Netherlands)},
volume = {19},
number = {},
pages = {100886},
pmid = {39287136},
issn = {2352-7714},
abstract = {In this multicenter study conducted in France, we challenged the hypothesis of the transmission of pathogens other than Borrelia spp. in 22 patients developing erythema migrans following a tick bite. Using a combination of high-throughput microfluidic PCRs and agnostic metagenomics on skin biopsies and blood samples, no microorganisms other than Borrelia spp. was found.},
}
@article {pmid39287058,
year = {2024},
author = {Irankhah, L and Khorsand, B and Naghibzadeh, M and Savadi, A},
title = {Analyzing the performance of short-read classification tools on metagenomic samples toward proper diagnosis of diseases.},
journal = {Journal of bioinformatics and computational biology},
volume = {},
number = {},
pages = {2450012},
doi = {10.1142/S0219720024500124},
pmid = {39287058},
issn = {1757-6334},
abstract = {Accurate knowledge of the genome, virus and bacteria that have invaded our bodies is crucial for diagnosing many human diseases. The field of bioinformatics encompasses the complex computational methods required for this purpose. Metagenomics employs next-generation sequencing (NGS) technology to study and identify microbial communities in environmental samples. This technique allows for the measurement of the relative abundance of different microbes. Various tools are available for detecting bacterial species in sequenced metagenomic samples. In this study, we focus on well-known taxonomic classification tools such as MetaPhlAn4, Centrifuge, Kraken2, and Bracken, and evaluate their performance at the species level using synthetic and real datasets. The results indicate that MetaPhlAn4 exhibited high precision in identifying species in the simulated dataset, while Kraken2 had the best area under the precision-recall curve (AUPR) performance. Centrifuge, Kraken2, and Bracken showed accurate estimation of species abundances, unlike MetaPhlAn4, which had a higher L2 distance. In the real dataset analysis with samples from an inflammatory bowel disease (IBD) research, MetaPhlAn4, and Kraken2 had faster execution times, with differences in performance at family and species levels among the tools. Enterobacteriaceae and Pasteurellaceae were highlighted as the most abundant families by Centrifuge, Kraken2, and MetaPhlAn4, with variations in abundance among ulcerative colitis (UC), Crohn's disease (CD), and control non-IBD (CN) groups. Escherichia coli (E. coli) has the highest abundance among Enterobacteriaceae species in the CD and UC groups in comparison with the CN group. Bracken overestimated E. coli abundance, emphasizing result interpretation caution. The findings of this research can assist in selecting the appropriate short-read classifier, thereby aiding in the diagnosis of target diseases.},
}
@article {pmid39286813,
year = {2024},
author = {Luo, J and An, N and Liu, Y and Li, Y},
title = {Disseminated emergomyces orientalis infection in a patient with systemic lupus erythematosus.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1401463},
pmid = {39286813},
issn = {2235-2988},
mesh = {Middle Aged ; Male ; Humans ; *Lupus Erythematosus, Systemic/complications ; Bone Marrow/pathology/microbiology ; Mycoses/microbiology/diagnosis ; Spores, Fungal ; },
abstract = {A case of Eimonosis orientalis was reported in a 52-year-old male farmer who presented with cough, phlegm, fever, headache, and nausea for more than 4 days. Haemophilic cells and fungal spores were identified in the bone marrow smear and confirmed as Aemon orientalis by culture. The same bacteria were also isolated from blood cultures.},
}
@article {pmid39286492,
year = {2024},
author = {Kouraki, A and Zheng, AS and Miller, S and Kelly, A and Ashraf, W and Bazzani, D and Bonadiman, A and Tonidandel, G and Bolzan, M and Vijay, A and Nightingale, J and Menni, C and Ollivere, BJ and Valdes, AM},
title = {Metagenomic changes in response to antibiotic treatment in severe orthopedic trauma patients.},
journal = {iScience},
volume = {27},
number = {9},
pages = {110783},
pmid = {39286492},
issn = {2589-0042},
abstract = {We investigated changes in microbiome composition and abundance of antimicrobial resistance (AMR) genes post-antibiotic treatment in severe trauma patients. Shotgun sequencing revealed beta diversity (Bray-Curtis) differences between 16 hospitalized multiple rib fractures patients and 10 age- and sex-matched controls (p = 0.043), and between antibiotic-treated and untreated patients (p = 0.015). Antibiotic-treated patients had lower alpha diversity (Shannon) at discharge (p = 0.003) and 12-week post-discharge (p = 0.007). At 12 weeks, they also exhibited a 5.50-fold (95% confidence interval [CI]: 2.86-8.15) increase in Escherichia coli (p = 0.0004) compared to controls. Differential analysis identified nine AMRs that increased in antibiotic-treated compared to untreated patients between hospital discharge and 6 and 12 weeks follow-up (false discovery rate [FDR] < 0.20). Two aminoglycoside genes and a beta-lactamase gene were directly related to antibiotics administered, while five were unrelated. In trauma patients, lower alpha diversity, higher abundance of pathobionts, and increases in AMRs persisted for 12 weeks post-discharge, suggesting prolonged microbiome disruption. Probiotic or symbiotic therapies may offer future treatment avenues.},
}
@article {pmid39284445,
year = {2024},
author = {Huo, C and Zhang, J and Yang, X and Li, X and Su, Y and Chen, Z},
title = {Dry season irrigation promotes nutrient cycling by reorganizing Eucalyptus rhizosphere microbiome.},
journal = {The Science of the total environment},
volume = {954},
number = {},
pages = {176307},
doi = {10.1016/j.scitotenv.2024.176307},
pmid = {39284445},
issn = {1879-1026},
abstract = {In southern China, seasonal droughts and low soil phosphorus content constrain the productivity of Eucalyptus trees. To understand the rhizosphere microbiome response to the dry season, metagenomic sequencing analysis was used to investigate the 6-year-old Eucalyptus rhizosphere microbiome under four different irrigation and fertilization treatments. The results showed that irrigation and fertilization during the dry season significantly altered the composition of microbiome in the rhizosphere soil of Eucalyptus plantations. The soil physicochemical properties and enzyme activity explained 30.73 % and 29.75 % of the changes in bacterial and fungal community structure in Eucalyptus rhizosphere soil, respectively. Irrigation and fertilization during the dry season significantly altered the physicochemical properties of rhizosphere soil. Compared with the seasonal drought without fertilizer treatment (CK), the dry season irrigation with fertilizer treatment (WF) significantly increased the content of total nitrogen (46.34 %), available nitrogen (37.72 %), available phosphorus (440.9 %), and organic matter (35.34 %). Soil organic matter (OM), pH, and available phosphorus (AP) were key environmental factors influencing the microbial community composition. Moreover, irrigation and fertilization promoted carbon fixation and nitrogen and phosphorus mineralization, increasing soil OM content and the availability of inorganic nitrogen and phosphorus. Meanwhile, compared to the CK, the increase of acid phosphatase (16.81 %), invertase (146.89 %)and urease (59.45 %) in rhizosphere soil under irrigation (W) treatment further proves that dry season irrigation promote the soil carbon, nitrogen and phosphorus cycles. Irrigation and fertilization treatment alleviated the constraints of low phosphorus in southern China's soil, which promoted Eucalyptus productivity. In conclusion, we suggest implementing reasonable irrigation and fertilization strategies in the production practice of Eucalyptus and utilizing microbial resources to improve soil fertility and Eucalyptus productivity.},
}
@article {pmid39284373,
year = {2024},
author = {Wu, Q and Deng, L and Lan, T and Wang, H and Wang, K and Zhu, H and Zhou, Y and Guo, W},
title = {Outstanding enhancement of caproate production with microwave pyrolyzed highly reductive biochar addition.},
journal = {Bioresource technology},
volume = {413},
number = {},
pages = {131457},
doi = {10.1016/j.biortech.2024.131457},
pmid = {39284373},
issn = {1873-2976},
abstract = {The integration of biochar into microbial Chain Elongation (CE) proves to be an effective tool of producing high-value bio-based products. This study innovatively applied biochar fabricated under microwave irradiation with carbon fiber cloth assistance into CE system. Results highlighted that microwave biochar achieved maximal CE efficiency yielding 8 g COD/L, with 3-fold increase to the blank group devoid of any biochar. Microwave biochar also obtained the highest substrate utilization rate of 94 %, while conventional biochar group recorded 90 % and the blank group was of 74 %. Mechanistic insights revealed that the reductive surface properties facilitated CE performance, which is relevant to fostering dominant genera of Parabacteroides, Bacteroides, and Macellibacteroides. By metagenomics, microwave biochar up-regulated functional genes and enzymes involved in CE process including ethanol oxidation, the reverse β-oxidation pathway, and the fatty acid biosynthesis pathway. This study effectively facilitated caproate production by utilizing a new microwave biochar preparation strategy.},
}
@article {pmid39283495,
year = {2024},
author = {Bellankimath, AB and Chapagain, C and Branders, S and Ali, J and Wilson, RC and Johansen, TEB and Ahmad, R},
title = {Culture and amplification-free nanopore sequencing for rapid detection of pathogens and antimicrobial resistance genes from urine.},
journal = {European journal of clinical microbiology &amp; infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {},
number = {},
pages = {},
pmid = {39283495},
issn = {1435-4373},
abstract = {PURPOSE: Urinary Tract Infections (UTIs) are among the most prevalent infections globally. Every year, approximately 150 million people are diagnosed with UTIs worldwide. The current state-of-the-art diagnostic methods are culture-based and have a turnaround time of 2-4 days for pathogen identification and susceptibility testing.<br><br>METHODS: This study first establishes an optical density culture-based method for spiking healthy urine samples with the six most prevalent uropathogens. Urine samples were spiked at clinically significant concentrations of 10[3]-10[5] CFU/ml. Three DNA extraction kits (BioStic, PowerFood, and Blood and Tissue) were investigated based on the DNA yield, average processing time, elution volume, and the average cost incurred per extraction. After DNA extraction, the samples were sequenced using MinION and Flongle flow cells.<br><br>RESULTS: The Blood and Tissue kit outperformed the other kits based on the investigated parameters. Using nanopore sequencing, all the pathogens and corresponding genes were only identified at a spike concentration of 10[5] CFU/ml, achieved after 10&#xa0;min and 3 hours of sequencing, respectively. However, some pathogens and antibiotic-resistance genes (ARG) could be identified from spikes at 10[3] colony formation units (CFU/mL). The overall turnaround time was five hours, from sample preparation to sequencing-based identification of pathogen ID and antimicrobial resistance genes.<br><br>CONCLUSION: This study demonstrates excellent promise in reducing the time required for informed antibiotic administration from 48 to 72&#xa0;h to five hours, thereby reducing the number of empirical doses and increasing the chance of saving lives.},
}
@article {pmid39283138,
year = {2024},
author = {Tarasov, K and Kravchenko, E and Zarubin, M and Yakhnenko, A},
title = {Deep underground metagenome-assembled genomes from hydrothermal spring.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0057424},
doi = {10.1128/mra.00574-24},
pmid = {39283138},
issn = {2576-098X},
abstract = {We report 19 metagenome-assembled genomes from a deep underground microbial community found in mineralized hydrothermal spring in the Baksan Neutrino Observatory tunnel. The community is predominantly occupied by members of Pseudomonadota (Gamma-, Beta-, and Alphaproteobacteria), Planctomycetota, Myxococcota, Nitrospirota, Cyanobacteria, Gemmatimonadota, and Armatimonadota.},
}
@article {pmid39283121,
year = {2024},
author = {Machado, DT and Dias, BdC and Cayô, R and Gales, AC and Marques de Carvalho, F and Vasconcelos, ATR},
title = {Uncovering new Firmicutes species in vertebrate hosts through metagenome-assembled genomes with potential for sporulation.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0211324},
doi = {10.1128/spectrum.02113-24},
pmid = {39283121},
issn = {2165-0497},
abstract = {Metagenome-assembled genomes (MAGs) have contributed to identifying non-culturable microorganisms and understanding their ecological functions. MAGs offer an advantage in investigating sporulation-associated genes, especially given the difficulty of isolating many species residing in the gut microbiota of multiple hosts. Bacterial sporulation is a key survival mechanism with implications for pathogenicity and biotechnology. Here, we investigate MAGs from vertebrate hosts, emphasizing taxonomic identification and identifying sporulation-associated genes in potential novel species within the Firmicutes phylum. We identified potential new species in the classes Clostridia (Borkfalkiaceae, Lachnospiraceae, Monoglobaceae, and Oscillospiraceae families) and Bacilli (Bacillaceae and Erysipelotrichaceae families) through phylogenetic and functional pathway analyses, highlighting their sporulation potential. Our study covers 146 MAGs, 124 of them without refined taxonomic assignments at the family level. We found that Clostridia and Bacilli have unique sporulation gene profiles in the refined family MAGs for cattle, swine, poultry, and human hosts. The presence of genes related to Spo0A regulon, engulfment, and spore cortex in MAGs underscores fundamental mechanisms in sporulation processes in currently uncharacterized species with sporulation potential from metagenomic dark matter. Furthermore, genomic analyses predict sporulation potential based on gene presence, genome size, and metabolic pathways involved in spore formation. We emphasize MAGs covering families not yet characterized through the phylogenetic analysis, and with extensive potential for spore-forming bacteria within Clostridia, Bacilli, UBA4882, and UBA994 classes. These findings contribute to exploring spore-forming bacteria, which provides evidence for novel species diversity in multiple hosts, their adaptive strategies, and potential applications in biotechnology and host health.IMPORTANCESpores are essential for bacterial survival in harsh environments, facilitating their persistence and adaptation. Exploring sporulation-associated genes in metagenome-assembled genomes (MAGs) from different hosts contributes to clinical and biotechnological domains. Our study investigated the extent of genes associated with bacterial sporulation in MAGs from poultry, swine, cattle, and humans, revealing these genes in uncultivated bacteria. We identified potential novel Firmicutes species with sporulation capabilities through phylogenetic and functional analyses. Notably, MAGs belonging to Clostridia, Bacilli, and unknown classes, namely UBA4882 and UBA994, remained uncharacterized at the family level, which raises the hypothesis that sporulation would also be present in these genomes. These findings contribute to our understanding of microbial adaptation and have implications for microbial ecology, underlining the importance of sporulation in Firmicutes across different hosts. Further studies into novel species and their sporulation capability can contribute to bacterial maintenance mechanisms in various organisms and their applications in biotechnology studies.},
}
@article {pmid39283083,
year = {2024},
author = {Brennan, C and Belda-Ferre, P and Zuffa, S and Charron-Lamoureux, V and Mohanty, I and Ackermann, G and Allaband, C and Ambre, M and Boyer, T and Bryant, M and Cantrell, K and Gonzalez, A and McDonald, D and Salido, RA and Song, SJ and Wright, G and Dorrestein, PC and Knight, R},
title = {Clearing the plate: a strategic approach to mitigate well-to-well contamination in large-scale microbiome studies.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0098524},
doi = {10.1128/msystems.00985-24},
pmid = {39283083},
issn = {2379-5077},
abstract = {UNLABELLED: Large-scale studies are essential to answer questions about complex microbial communities that can be extremely dynamic across hosts, environments, and time points. However, managing acquisition, processing, and analysis of large numbers of samples poses many challenges, with cross-contamination being the biggest obstacle. Contamination complicates analysis and results in sample loss, leading to higher costs and constraints on mixed sample type study designs. While many researchers opt for 96-well plates for their workflows, these plates present a significant issue: the shared seal and weak separation between wells leads to well-to-well contamination. To address this concern, we propose an innovative high-throughput approach, termed as the Matrix method, which employs barcoded Matrix Tubes for sample acquisition. This method is complemented by a paired nucleic acid and metabolite extraction, utilizing 95% (vol/vol) ethanol to stabilize microbial communities and as a solvent for extracting metabolites. Comparative analysis between conventional 96-well plate extractions and the Matrix method, measuring 16S rRNA gene levels via quantitative polymerase chain reaction, demonstrates a notable decrease in well-to-well contamination with the Matrix method. Metagenomics, 16S rRNA gene amplicon sequencing (16S), and untargeted metabolomics analysis via liquid chromatography-tandem mass spectrometry (LC-MS/MS) confirmed that the Matrix method recovers reproducible microbial and metabolite compositions that can distinguish between subjects. This advancement is critical for large-scale study design as it minimizes well-to-well contamination and technical variation, shortens processing times, and integrates with automated infrastructure for enhancing sample randomization and metadata generation.<br><br>IMPORTANCE: Understanding dynamic microbial communities typically requires large-scale studies. However, handling large numbers of samples introduces many challenges, with cross-contamination being a major issue. It not only complicates analysis but also leads to sample loss and increased costs and restricts diverse study designs. The prevalent use of 96-well plates for nucleic acid and metabolite extractions exacerbates this problem due to their wells having little separation and being connected by a single plate seal. To address this, we propose a new strategy using barcoded Matrix Tubes, showing a significant reduction in cross-contamination compared to conventional plate-based approaches. Additionally, this method facilitates the extraction of both nucleic acids and metabolites from a single tubed sample, eliminating the need to collect separate aliquots for each extraction. This innovation improves large-scale study design by shortening processing times, simplifying analysis, facilitating metadata curation, and producing more reliable results.},
}
@article {pmid39283018,
year = {2024},
author = {Yu, H and Liu, S and Weng, W and Peng, Y and Cai, X and Zhu, Y and Chen, P and Zhang, D and Liu, H and Zeng, J and Liu, S and He, Z and Yan, Q},
title = {Generational Specific Recruitment of Arsenic- and Antimony-Reducing Microorganisms in Plant Root-Associated Niches for Adapting to Metalloid-Metal Pollution.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c05291},
pmid = {39283018},
issn = {1520-5851},
abstract = {The recruitment of microorganisms by plants can enhance their adaptability to environmental stressors, but how root-associated niches recruit specific microorganisms for adapting to metalloid-metal contamination is not well-understood. This study investigated the generational recruitment of microorganisms in different root niches of Vetiveria zizanioides (V. zizanioides) under arsenic (As) and antimony (Sb) stress. The V. zizanioides was cultivated in As- and Sb-cocontaminated mine soils (MS) and artificial pollution soils (PS) over two generations in controlled conditions. The root-associated microbial communities were analyzed through 16S rRNA, arsC, and aioA gene amplicon and metagenomics sequencing. V. zizanioides accumulated higher As(III) and Sb(III) in its endosphere in MS in the second generation, while its physiological indices in MS were better than those observed in PS. SourceTracker analysis revealed that V. zizanioides in MS recruited As(V)- and Sb(V)-reducing microorganisms (e.g., Sphingomonales and Rhodospirillaceae) into the rhizoplane and endosphere. Metagenomics analysis further confirmed that these recruited microorganisms carrying genes encoding arsenate reductases with diverse carbohydrate degradation abilities were enriched in the rhizoplane and endosphere, suggesting their potential to reduce As(V) and Sb(V) and to decompose root exudates (e.g., xylan and starch). These findings reveal that V. zizanioides selectively recruits As- and Sb-reducing microorganisms to mitigate As-Sb cocontamination during the generational growth, providing insights into novel strategies for enhancing phytoremediation of metalloid-metal contaminants.},
}
@article {pmid39282562,
year = {2024},
author = {Chang, Y and Zhang, Z and Cai, J and Wang, C and Liu, D and Liu, Z and Xu, C},
title = {Coevolution of specific gut microbiota of Min pig with host cold adaptation through enhanced vitamin B1 synthesis.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1448090},
pmid = {39282562},
issn = {1664-302X},
abstract = {Min pigs exhibit remarkable cold tolerance, where vitamin B1 synthesis by gut microbiota is crucial for the host's energy metabolism. However, the role of this synthesis in cold adaptation of Min pigs are not yet fully understood. This study utilized 16S rRNA amplicon and metagenomic sequencing to examine seasonal variations in the gut microbiota of Min pigs. Results indicated a significant rise in microbial diversity in winter, with the Bacteroidetes group being the most notably increased. The vitamin B1 biosynthetic pathway was significantly enriched during winter, with six significantly upregulated genes (ThiC, ThiD, ThiE, ThiG, ThiH, and ThiL) showing strong evidence of purifying selection. Among the six vitamin B1 synthesis genes significantly upregulated during winter, the increase was mainly due to a marked elevation in several sequences from specific microbial species. Binding energy analysis revealed that, except for ThiL, the average substrate binding energy of the top 10 sequences with the largest seasonal differences was significantly lower than those of the 10 sequences with the smallest differences. Furthermore, most of these sequences were uniquely prevalent in Min pigs and were not found in the homologous sequences of Duroc pigs. Bacteroidetes and Bacteroidales were identified as the primary contributors to these gene sequences. This research provides valuable insights for developing innovative cold-resistant feed and probiotics.},
}
@article {pmid39282334,
year = {2024},
author = {Olivos-Caicedo, KY and Fernandez, F and Daniel, SL and Anantharaman, K and Ridlon, JM and Alves, JMP},
title = {Pangenome analysis of Clostridium scindens : a collection of diverse bile acid and steroid metabolizing commensal gut bacterial strains.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.09.06.610859},
pmid = {39282334},
issn = {2692-8205},
abstract = {Clostridium scindens is a commensal gut bacterium capable of forming the secondary bile acids deoxycholic acid and lithocholic acid from the primary bile acids cholic acid and chenodeoxycholic acid, respectively, as well as converting glucocorticoids to androgens. Historically, only two strains, C. scindens ATCC 35704 and C. scindens VPI 12708, have been characterized in vitro and in vivo to any significant extent. The formation of secondary bile acids is important in maintaining normal gastrointestinal function, in regulating the structure of the gut microbiome, in the etiology of such diseases such as cancers of the GI tract, and in the prevention of Clostridium difficile infection. We therefore wanted to determine the pangenome of 34 cultured strains of C. scindens and a set of 200 metagenome-assembled genomes (MAGs) to understand the variability among strains. The results indicate that the 34 strains of C. scindens have an open pangenome with 12,720 orthologous gene groups, and a core genome with 1,630 gene families, in addition to 7,051 and 4,039 gene families in the accessory and unique (i.e., strain-exclusive) genomes, respectively. The core genome contains 39% of the proteins with predicted metabolic function, and, in the unique genome, the function of storage and processing of information prevails, with 34% of the proteins being in that category. The pangenome profile including the MAGs also proved to be open. The presence of bile acid inducible (bai) and steroid-17,20-desmolase (des) genes was identified among groups of strains. The analysis reveals that C. scindens strains are distributed into two clades, indicating the possible onset of C. scindens separation into two species, confirmed by gene content, phylogenomic, and average nucleotide identity (ANI) analyses. This study provides insight into the structure and function of the C. scindens pangenome, offering a genetic foundation of significance for many aspects of research on the intestinal microbiota and bile acid metabolism.},
}
@article {pmid39282326,
year = {2024},
author = {Ramani, S and Javornik Cregeen, SJ and Surathu, A and Neill, FH and Muzny, DM and Doddapaneni, H and Menon, VK and Hoffman, KL and Ross, MC and Metcalf, G and Opekun, AR and Graham, DY and Gibbs, RA and Petrosino, JF and Estes, MK and Atmar, RL},
title = {INTRA- AND INTER-HOST EVOLUTION OF HUMAN NOROVIRUS IN HEALTHY ADULTS.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39282326},
issn = {2692-8205},
support = {P01 AI057788/AI/NIAID NIH HHS/United States ; U19 AI144297/AI/NIAID NIH HHS/United States ; },
abstract = {BACKGROUND: Human noroviruses are a leading cause of acute and sporadic gastroenteritis worldwide. The evolution of human noroviruses in immunocompromised persons has been evaluated in many studies. Much less is known about the evolutionary dynamics of human norovirus in healthy adults.<br><br>METHODS: We used sequential samples collected from a controlled human infection study with GI.1/Norwalk/US/68 virus to evaluate intra- and inter-host evolution of a human norovirus in healthy adults. Up to 12 samples from day 1 to day 56 post-challenge were sequenced using a norovirus-specific capture probe method.<br><br>RESULTS: Complete genomes were assembled, even in samples that were below the limit of detection of standard RT-qPCR assays, up to 28 days post-challenge. Analysis of 123 complete genomes showed changes in the GI.1 genome in all persons, but there were no conserved changes across all persons. Single nucleotide variants resulting in non-synonymous amino acid changes were observed in all proteins, with the capsid VP1 and nonstructural protein NS3 having the largest numbers of changes.<br><br>CONCLUSIONS: These data highlight the potential of a new capture-based sequencing approach to assemble human norovirus genomes with high sensitivity and demonstrate limited conserved immune pressure-driven evolution of GI.1 virus in healthy adults.},
}
@article {pmid39282201,
year = {2024},
author = {Lata, P and Bhargava, V and Gupta, S and Singh, A and Bala, K and Lal, R},
title = {SeqCode: A Nomenclatural Code for Prokaryotes.},
journal = {Indian journal of microbiology},
volume = {64},
number = {3},
pages = {859-866},
pmid = {39282201},
issn = {0046-8991},
abstract = {SeqCode is a nomenclatural code for naming prokaryotes based on genetic information. With the majority of prokaryotes being inaccessible as pure cultures, they are not eligible for naming under the International Code of Nomenclature of Prokaryotes. To address this challenge, a new concept that is SeqCode, which assign names to prokaryotes on the basis of genome sequence, has been announced in 2022. The valid publication of names for prokaryotes based on isolated genome, metagenome-assembled genomes, or single-amplified genome sequences. It operates through a registration portal, SeqCode Registry, where metadata is linked to names and nomenclatural types. This code provides a framework for reproducible nomenclature for all prokaryotes, either culturable or not and facilitates communication across all microbiological disciplines. Additionally, the SeqCode includes provisions for updating and revising names as new data becomes available. By providing a standardized system for naming and classifying these microorganisms based on their genetic information, the SeqCode will facilitate the discovery, understanding and comparison of these microorganisms, helping us to understand their role in the environment and how they contribute to the functioning of the Earth.},
}
@article {pmid39282167,
year = {2024},
author = {Rangra, S and Sharma, N and Lata, P and Sharma, KB and Kumari, R and Singh, SP and Savitri, },
title = {NGS-Based Metagenomics Depicting Taxonomic and Functional Insights into North-Western Himalayan Hot Springs.},
journal = {Indian journal of microbiology},
volume = {64},
number = {3},
pages = {1099-1109},
pmid = {39282167},
issn = {0046-8991},
abstract = {UNLABELLED: Hot springs have tremendous significance due to their divulging physiochemical features. In the recent past, metagenomics has emerged as a unique methodology to explore microbiota as well as new biocatalysts possessing advantageous biochemical properties from hot springs. In the present study, metagenomics has been employed for microbial diversity exploration and identification of genes involved in various metabolic pathways among two hot springs, Manikaran and Tatapani, located in Himachal Pradesh, India. Taxonomic analysis of both metagenomes revealed the dominance of the Proteobacteria phylum. Genomic signatures of other bacterial phyla such as Chloroflexi, Actinobacteria, Bacteroidetes, Cyanobacteria, Planctomycetes, and Firmicutes were also found in significant abundance in both the metagenomes. The abundance of microorganisms belonging to genera, especially Nitrospira, Thauera, Meiothermus, Thiobacillus, Massilia, and Anaerolinea, was reported to be prevalent in the hot springs. A significant amount of metagenomic data remained taxonomically unclassified, which indeed emphasizes the scientific importance of these thermoaquatic niches. The functional potential analysis of both metagenomes revealed pathways related to carbohydrate metabolism, followed by amino acid metabolism, energy metabolism, genetic information processing, metabolism of cofactors and vitamins, membrane transporter, and signal transduction. Exploration of biomass-modifying biocatalysts enumerated the presence of glycoside hydrolases, glycosyl transferases, polysaccharide lyases, and carbohydrate esterases in the metagenomic data. Together, these findings offer an in-depth understanding of the microbial inhabitants in North-Western Himalayan hot springs and their underlying potential for various biotechnological and industrial applications.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12088-024-01248-z.},
}
@article {pmid39281749,
year = {2024},
author = {Kang, JW and Khatib, LA and Heston, MB and Dilmore, AH and Labus, JS and Deming, Y and Schimmel, L and Blach, C and McDonald, D and Gonzalez, A and Bryant, M and Sanders, K and Schwartz, A and Ulland, TK and Johnson, SC and Asthana, S and Carlsson, CM and Chin, NA and Blennow, K and Zetterberg, H and Rey, FE and , and Kaddurah-Daouk, R and Knight, R and Bendlin, BB},
title = {Gut Microbiome Compositional and Functional Features Associate with Alzheimer's Disease Pathology.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
pmid = {39281749},
support = {U19 AG063744/AG/NIA NIH HHS/United States ; S10 OD026929/OD/NIH HHS/United States ; U01 AG061359/AG/NIA NIH HHS/United States ; P30 AG062715/AG/NIA NIH HHS/United States ; R01 AG083883/AG/NIA NIH HHS/United States ; R01 AG070973/AG/NIA NIH HHS/United States ; },
abstract = {BACKGROUND: The gut microbiome is a potentially modifiable factor in Alzheimer's disease (AD); however, understanding of its composition and function regarding AD pathology is limited.<br><br>METHODS: Shallow-shotgun metagenomic data was used to analyze fecal microbiome from participants enrolled in the Wisconsin Microbiome in Alzheimer's Risk Study, leveraging clinical data and cerebrospinal fluid (CSF) biomarkers. Differential abundance and ordinary least squares regression analyses were performed to find differentially abundant gut microbiome features and their associations with CSF biomarkers of AD and related pathologies.<br><br>RESULTS: Gut microbiome composition and function differed between people with AD and cognitively unimpaired individuals. The compositional difference was replicated in an independent cohort. Differentially abundant gut microbiome features were associated with CSF biomarkers of AD and related pathologies.<br><br>DISCUSSION: These findings enhance our understanding of alterations in gut microbial composition and function in AD, and suggest that gut microbes and their pathways are linked to AD pathology.},
}
@article {pmid39281597,
year = {2024},
author = {Yuan, X and Zhang, D and Li, D and Ji, Q and Gao, J and Hou, F and Chen, Y},
title = {Metagenomic and metabolite analysis reveals microbial community and metabolite dynamics in fermented Indigo naturalis.},
journal = {Heliyon},
volume = {10},
number = {17},
pages = {e36733},
pmid = {39281597},
issn = {2405-8440},
abstract = {The soaking and fermentation of the stems and leaves is an important intermediate step in the processing of Indigo Naturalis. However, the relationship between microbiota and Indigo Naturalis yields is still poorly understood. This study aimed to compare microbial communities and metabolite profiles at various stages of soaking fermentation, followed by validation of the results using HPLC. A total of 731 compounds were identified through metabolite analysis, with the levels of indigo and indirubin peaking after 36 h of fermentation. Metagenomes revealed Firmicutes, Proteobacteria, Bacteroidetes and Actinobacteria were identified as the most abundant microbial phyla in soaking fermentation. Correlation analysis indicated that the yields of indigo and indirubin may be affected by Lactococcus, Clostridium, and Enterobacter through the regulation of related synthetic enzymes. The findings offered novel perspectives on the relationship of microorganisms and Indigo Naturalis yields.},
}
@article {pmid39281050,
year = {2024},
author = {Yang, Z and Zheng, Y and Liu, S and Xie, T and Wang, Q and Wang, Z and Li, S and Wang, W},
title = {Rumen metagenome reveals the mechanism of mitigation methane emissions by unsaturated fatty acid while maintaining the performance of dairy cows.},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {18},
number = {},
pages = {296-308},
pmid = {39281050},
issn = {2405-6383},
abstract = {Dietary fat content can reduce the methane production of dairy cows; however, the relevance fatty acid (FA) composition has towards this inhibitory effect is debatable. Furthermore, in-depth studies elucidating the effects of unsaturated fatty acids (UFA) on rumen function and the mechanism of reducing methane (CH4) production are lacking. This study exposed 10 Holstein cows with the same parity, similar milk yield to two total mixed rations: low unsaturated FA (LUFA) and high unsaturated FA (HUFA) with similar fat content. The LUFA group mainly added fat powder (C16:0 > 90%), and the HUFA group mainly replaced fat powder with extruded flaxseed. The experiment lasted 26 d, the last 5 d of which, gas exchange in respiratory chambers was conducted to measure gas emissions. We found that an increase in the UFA in diet did not affect milk production (P > 0.05) and could align the profile of milk FAs more closely with modern human nutritional requirements. Furthermore, we found that increasing the UFA content in the diet lead to a decrease in the abundance of Methanobrevibacter in the rumen (|linear discriminant analysis [LDA] score| > 2 and P < 0.05), which resulted in a decrease in the relative abundance of multiple enzymes (EC:1.2.7.12, EC:2.3.1.101, EC:3.5.4.27, EC:1.5.98.1, EC:1.5.98.2, EC:6.2.1.1, EC:2.1.1.86 and EC:2.8.4.1) during methanogenesis (P < 0.05). Compared with the LUFA group, the pathway of CH4 metabolism was inhibited in the HUFA group (|LDA| > 2 and P < 0.05), which ultimately decreased CH4 production (P < 0.05). Our results illustrated the mechanism involving decreased CH4 production when fed a UFA diet in dairy cows. We believe that our study provides new evidence to explore CH4 emission reduction measures for dairy cows.},
}
@article {pmid39280079,
year = {2024},
author = {Lindner, BG and Choudhury, RA and Pinamang, P and Bingham, L and D'Amico, I and Hatt, JK and Konstantinidis, KT and Graham, KE},
title = {Advancing Source Tracking: Systematic Review and Source-Specific Genome Database Curation of Fecally Shed Prokaryotes.},
journal = {Environmental science &amp; technology letters},
volume = {11},
number = {9},
pages = {931-939},
pmid = {39280079},
issn = {2328-8930},
abstract = {Advancements within fecal source tracking (FST) studies are complicated by a lack of knowledge regarding the genetic content and distribution of fecally shed microbial populations. To address this gap, we performed a systematic literature review and curated a large collection of genomes (n = 26,018) representing fecally shed prokaryotic species across broad and narrow source categories commonly implicated in FST studies of recreational waters (i.e., cats, dogs, cows, seagulls, chickens, pigs, birds, ruminants, human feces, and wastewater). We find that across these sources the total number of prokaryotic genomes recovered from materials meeting our initial inclusion criteria varied substantially across fecal sources: from none in seagulls to 9,085 in pigs. We examined genome sequences recovered from these metagenomic and isolation-based studies extensively via comparative genomic approaches to characterize trends across source categories and produce a finalized genome database for each source category which is available online (n = 12,730). On average, 81% of the genomes representing species-level populations occur only within a single source. Using fecal slurries to test the performance of each source database, we report read capture rates that vary with fecal source alpha diversity and database size. We expect this resource to be useful to FST-related objectives, One Health research, and sanitation efforts globally.},
}
@article {pmid39277915,
year = {2024},
author = {Zeng, X and Tang, S and Dong, X and Dong, M and Shao, R and Liu, R and Li, T and Zhang, X and Wong, YH and Xie, Q},
title = {Corrigendum to "Analysis of metagenome and metabolome disclosed the mechanisms of Dendrobium officinale polysaccharide on DSS-induced ulcerative colitis-affected mice" [Int. J. Biol. Macromol. 277 (2024) 134229].},
journal = {International journal of biological macromolecules},
volume = {279},
number = {Pt 4},
pages = {135575},
doi = {10.1016/j.ijbiomac.2024.135575},
pmid = {39277915},
issn = {1879-0003},
}
@article {pmid39277616,
year = {2024},
author = {Jia, Y and Shi, Y and Wang, J and Liu, H and Huang, Y and Wang, H and Liu, Y and Peng, J},
title = {Integrating metagenomics with metabolomics for gut microbiota and metabolites profiling in acute pancreatitis.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {21491},
pmid = {39277616},
issn = {2045-2322},
support = {GZC20242045//Postdoctoral Fellowship Program of CPSF/ ; 2023zzts896//Fundamental Research Funds for Central Universities of the Central South University/ ; 82170661//National Natural Science Foundation of China/ ; 2023DK2002//Key Project of Research and Development Plan of Hunan Province/ ; },
mesh = {*Gastrointestinal Microbiome ; *Pancreatitis/microbiology/metabolism ; Animals ; *Metabolomics/methods ; *Metagenomics/methods ; Mice ; Metabolome ; Disease Models, Animal ; Dysbiosis/microbiology/metabolism ; Mice, Inbred C57BL ; Male ; Acute Disease ; },
abstract = {Acute pancreatitis (AP) is an inflammatory disease of the pancreas. Despite of a steadily increasing in morbidity and mortality, there is still no effective therapy. Gut microbial dysbiosis and its derived-metabolites disorder have been shown to play an important role in the development of AP, however, little is known regarding the crosstalk between gut microbiota and metabolites. In this study, we assessed the alterations in gut microbiota and metabolites by constructing three AP mouse models by means of metagenomic and metabolomic sequencing, and further clarified their relationship by correlation analysis. The results revealed that each model exhibited unique flora and metabolite profiles. KEGG analysis showed that the differential flora and metabolite-enriched pathway functions were correlated with lipid metabolism and amino acid metabolism. Moreover, two core differential bacterial species on Burkholderiales bacterium YL45 and Bifidobacterium pseudolongum along with eleven differential metabolites appeared to exert certain effects during the course of AP. In conclusion, further exploration of the crosstalk between microbiota and derived metabolites may provide novel insights and strategies into the diagnosis and treatment of AP.},
}
@article {pmid39277613,
year = {2024},
author = {da Silva, S and Vuong, P and Amaral, JRV and da Silva, VAS and de Oliveira, SS and Vermelho, AB and Beale, DJ and Bissett, A and Whiteley, AS and Kaur, P and Macrae, A},
title = {The piranha gut microbiome provides a selective lens into river water biodiversity.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {21518},
pmid = {39277613},
issn = {2045-2322},
support = {Bolsa de Doutorado//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; Bolsa de Iniciacao Cientifica//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; Bolsa de doutordo//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; PRINT 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; },
mesh = {*Rivers/microbiology ; *Gastrointestinal Microbiome/genetics ; Animals ; *Biodiversity ; Metagenome ; Metagenomics/methods ; Water Microbiology ; Bacteria/genetics/classification/isolation &amp; purification ; },
abstract = {Advances in omics technologies have enabled the in-depth study of microbial communities and their metabolic profiles from all environments. Here metagenomes were sampled from piranha (Serrasalmus rhombeus) and from river water from the Rio São Benedito (Amazon Basin). Shotgun metagenome sequencing was used to explore diversity and to test whether fish microbiomes are a good proxy for river microbiome studies. The results showed that the fish microbiomes were not significantly different from the river water microbiomes at higher taxonomic ranks. However, at the genus level, fish microbiome alpha diversity decreased, and beta diversity increased. This result repeated for functional gene abundances associated with specific metabolic categories (SEED level 3). A clear delineation between water and fish was seen for beta diversity. The piranha microbiome provides a good and representative subset of its river water microbiome. Variations seen in beta biodiversity were expected and can be explained by temporal variations in the fish microbiome in response to stronger selective forces on its biodiversity. Metagenome assembled genomes construction was better from the fish samples. This study has revealed that the microbiome of a piranha tells us a lot about its river water microbiome and function.},
}
@article {pmid39277504,
year = {2024},
author = {Fida, M and Tande, AJ},
title = {State-of-the-Art Metagenomic Sequencing and Its Role in the Diagnosis of Periprosthetic Joint Infections.},
journal = {Infectious disease clinics of North America},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.idc.2024.07.011},
pmid = {39277504},
issn = {1557-9824},
abstract = {Metagenomic next-generation sequencing (mNGS) is increasingly being recognized as a valuable diagnostic tool for periprosthetic joint infections (PJIs). This study reviews the diagnostic utility of mNGS, highlighting its improved sensitivity in detecting pathogens, particularly in culture-negative and polymicrobial infections. However, the clinical application of this method is hindered by challenges such as the prevalence of host DNA, the necessity for extensive bioinformatic analysis, and the potential for contamination, which can lead to misinterpretation of results. As mNGS continues to evolve, it holds significant potential to improve the management of PJI and enhance the application of precision medicine in orthopedic infections.},
}
@article {pmid39276831,
year = {2024},
author = {Li, C and Zhang, Y and Shi, W and Peng, Y and Han, Y and Jiang, S and Dong, X and Zhang, R},
title = {Viral diversity within marine biofilms and interactions with corrosive microbes.},
journal = {Environmental research},
volume = {263},
number = {Pt 1},
pages = {119991},
doi = {10.1016/j.envres.2024.119991},
pmid = {39276831},
issn = {1096-0953},
abstract = {In marine environments, a wide variety of microbes like bacteria, and archaea influence on the corrosion of materials. Viruses are widely distributed in biofilms among these microbes and may affect the corrosion process through interactions with key corrosive prokaryotes. However, understanding of the viral communities within biofilms and their interactions with corrosive microbes remains is limited. To improve this knowledge gap, 53 metagenomes were utilized to investigate the diversity of viruses within biofilms on 8 different materials and their interactions with corrosive microbes. Notably, the viruses within biofilms predominantly belonged to Caudoviricetes, and phylogenetic analysis of Caudoviricetes and protein-sharing networks with other environments revealed the presence of numerous novel viral clades in biofilms. The virus‒host linkages revealed a close association between viruses and corrosive microbes in biofilms. This means that viruses may modulate host corrosion-related metabolism through auxiliary metabolic genes. It was observed that the virus could enhance host resistance to metals and antibiotics via horizontal gene transfer. Interestingly, viruses could protect themselves from host antiviral systems through anti-defense systems. This study illustrates the diversity of viruses within biofilms formed on materials and the intricate interactions between viruses and corrosive microbes, showing the potential roles of viruses in corrosive biofilms.},
}
@article {pmid39276741,
year = {2024},
author = {Kumar, A and Lakhawat, SS and Singh, K and Kumar, V and Verma, KS and Dwivedi, U and Kothari, SL and Malik, N and Sharma, PK},
title = {Metagenomic analysis of soil from landfill site reveals a diverse microbial community involved in plastic degradation.},
journal = {Journal of hazardous materials},
volume = {480},
number = {},
pages = {135804},
doi = {10.1016/j.jhazmat.2024.135804},
pmid = {39276741},
issn = {1873-3336},
abstract = {In this study, we have investigated microbial communities structure and function using high throughput amplicon sequencing and whole metagenomic sequencing of DNA extracted from different depths of a plastic-laden landfill site. With diverse taxonomic groups inhabiting the plastic-rich soil, our study demonstrates the remarkable adaptability of microbes to use this new substrate as a carbon source. FTIR spectroscopic analysis of soil indicated degradation of plastic as perceived from the carbonyl index of 0.16, 0.72, and 0.44 at 0.6, 0.9 and 1.2 m depth, respectively. Similarly, water contact angles of 108.7 degree, 99.7 degree, 62.7 degree, and 77.8 degree of plastic pieces collected at 0.3, 0.6, 0.9, and 1.2 m depths respectively showed increased wettability and hydrophilicity of the plastic. Amplicon analysis of 16S and 18 S rRNA revealed a high abundance of several plastic-degrading bacterial groups, including Pseudomonas, Rhizobiales, Micrococcaceae, Chaetomium, Methylocaldum, Micromonosporaceae, Rhodothermaceae and fungi, including Trichoderma, Aspergillus, Candida at 0.9 m. The co-existence of specific microbial groups at different depths of landfill site indicates importance of bacterial and fungal interactions for plastic. Whole metagenome analysis of soil sample at 0.9 m depth revealed a high abundance of genes encoding enzymes that participate in the biodegradation of PVC, polyethylene, PET, and polyurethane. Curation of the pathways related to the degradation of these materials provided a blueprint for plastic biodegradation in this ecosystem. Altogether, our study has highlighted the importance of microbial cooperation for the biodegradation of pollutants. Our metagenome-based investigation supports the current perception that consortia of fungi-bacteria are preferable to axenic cultures for effective bioremediation of the environment.},
}
@article {pmid39276731,
year = {2024},
author = {Shan, M and Zheng, C and Song, J and Qiu, M and Huang, C and Cui, M and Wang, J and Chen, W and Zhang, L and Yu, Y and Fang, H},
title = {Biochar and theaflavins mitigate the antibiotic resistome and antibiotic-resistant pathogens in a soil-lettuce continuum.},
journal = {Journal of hazardous materials},
volume = {480},
number = {},
pages = {135821},
doi = {10.1016/j.jhazmat.2024.135821},
pmid = {39276731},
issn = {1873-3336},
abstract = {Antibiotic resistance can be transferred into the food chain, leading to increased risks to human health from ready-to-eat vegetables. Mitigating the transmission of antibiotic resistance from soil to vegetables by green materials is of great significance. Here, we deciphered the roles of biochar and theaflavins in mitigating antibiotic resistance genes (ARGs) and antibiotic-resistant pathogens (ARPs) in a soil-lettuce continuum. Metagenomic results showed that biochar led to a significant decrease in the abundance of ARGs in lettuce leaves, while theaflavins contributed to a significant reduction in the diversity and abundance of ARGs in soil, particularly targeting dominant ARG types such as sulfonamide and aminoglycoside resistance genes. Meanwhile, biochar and theaflavins alleviated the potential mobility of ARGs, in lettuce leaves and soil, respectively, including the spread of ARGs to human pathogens. In addition, the diversity of ARG hosts was reduced in the soil-lettuce continuum and ARPs were not detected in lettuce leaves after the application of biochar or theaflavins. Overall, this study provides a novel perspective on green materials for mitigating the antibiotic resistome and ARPs in the soil-lettuce continuum, contributing to food security and human health.},
}
@article {pmid39267516,
year = {2024},
author = {Liu, YZ and Zhang, R and Xie, JJ and Guo, Q and Zhan, CX and Chen, MY and Li, JS and Peng, XM},
title = {[Two cases of neonatal Legionella pneumonia].},
journal = {Zhongguo dang dai er ke za zhi = Chinese journal of contemporary pediatrics},
volume = {26},
number = {9},
pages = {986-988},
pmid = {39267516},
issn = {1008-8830},
mesh = {Humans ; Female ; Infant, Newborn ; *Legionnaires' Disease/diagnosis/drug therapy ; },
abstract = {Patient 1, a 12-day-old female infant, presented with fever, cough, dyspnea, and elevated infection markers, requiring respiratory support. Metagenomic next-generation sequencing (mNGS) of blood and bronchoalveolar lavage fluid revealed Legionella pneumophila (LP), leading to diagnoses of LP pneumonia and LP sepsis. The patient was treated with erythromycin for 15 days and azithromycin for 5 days, resulting in recovery and discharge. Patient 2, an 11-day-old female infant, presented with dyspnea, fever, elevated infection markers, and multiple organ dysfunction, requiring mechanical ventilation. mNGS of blood and cerebrospinal fluid indicated LP, leading to diagnoses of LP pneumonia, LP sepsis, and LP intracranial infection. The patient was treated with erythromycin for 19 days and was discharged after recovery. Neonatal LP pneumonia lacks specific clinical symptoms, and azithromycin is the preferred antimicrobial agent. The use of mNGS can provide early and definitive diagnosis for severe neonatal pneumonia of unknown origin.},
}
@article {pmid39267333,
year = {2024},
author = {Fujii, N and Kuroda, K and Narihiro, T and Aoi, Y and Ozaki, N and Ohashi, A and Kindaichi, T},
title = {Unique episymbiotic relationship between Candidatus Patescibacteria and Zoogloea in activated sludge flocs at a municipal wastewater treatment plant.},
journal = {Environmental microbiology reports},
volume = {16},
number = {5},
pages = {e70007},
pmid = {39267333},
issn = {1758-2229},
support = {23KJ16420A//JSPS KAKENHI/ ; JP16H04833//JSPS KAKENHI/ ; JP20H02287//JSPS KAKENHI/ ; },
mesh = {*Sewage/microbiology ; *Symbiosis ; *Zoogloea/genetics/metabolism ; *Wastewater/microbiology ; In Situ Hybridization, Fluorescence ; Metagenome ; Phylogeny ; },
abstract = {Candidatus Patescibacteria, also known as candidate phyla radiation (CPR), including the class-level uncultured clade JAEDAM01 (formerly a subclass of Gracilibacteria/GN02/BD1-5), are ubiquitous in activated sludge. However, their characteristics and relationships with other organisms are largely unknown. They are believed to be episymbiotic, endosymbiotic or predatory. Despite our understanding of their limited metabolic capacity, their precise roles remain elusive due to the difficulty in cultivating and identifying them. In previous research, we successfully recovered high-quality metagenome-assembled genomes (MAGs), including a member of JAEDAM01 from activated sludge flocs. In this study, we designed new probes to visualize the targeted JAEDAM01-associated MAG HHAS10 and identified its host using fluorescence in situ hybridization (FISH). The FISH observations revealed that JAEDAM01 HHAS10-like cells were located within dense clusters of Zoogloea, and the fluorescence brightness of zoogloeal cells decreased in the vicinity of the CPR cells. The Zoogloea MAGs possessed genes related to extracellular polymeric substance biosynthesis, floc formation and nutrient removal, including a polyhydroxyalkanoate (PHA) accumulation pathway. The JAEDAM01 MAG HHAS10 possessed genes associated with type IV pili, competence protein EC and PHA degradation, suggesting a Zoogloea-dependent lifestyle in activated sludge flocs. These findings indicate a new symbiotic relationship between JAEDAM01 and Zoogloea.},
}
@article {pmid39267241,
year = {2024},
author = {Doni, L and Azzola, A and Oliveri, C and Bosi, E and Auguste, M and Morri, C and Bianchi, CN and Montefalcone, M and Vezzulli, L},
title = {Genome-resolved metagenomics revealed novel microbial taxa with ancient metabolism from macroscopic microbial mat structures inhabiting anoxic deep reefs of a Maldivian Blue Hole.},
journal = {Environmental microbiology reports},
volume = {16},
number = {5},
pages = {e13315},
pmid = {39267241},
issn = {1758-2229},
support = {CN_00000033//Centro Nazionale di Ricerca - Biodiversit&#xe0; (Italy) project (PNRR CN00000033 - Centro Nazionale Biodiversit&#xe0;/ ; CUP D33C22000960007//Italian Ministry of University and Research/ ; },
mesh = {*Metagenomics ; *Phylogeny ; *Metagenome ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Geologic Sediments/microbiology ; Genome, Bacterial/genetics ; Anaerobiosis ; Deltaproteobacteria/genetics/classification/isolation &amp; purification/metabolism ; Chloroflexi/genetics/classification/isolation &amp; purification/metabolism ; Proteobacteria/genetics/classification/isolation &amp; purification ; Microbiota ; },
abstract = {Blue holes are vertical water-filled openings in carbonate rock that exhibit complex morphology, ecology, and water chemistry. In this study, macroscopic microbial mat structures found in complete anoxic conditions in the Faanu Mudugau Blue Hole (Maldives) were studied by metagenomic methods. Such communities have likely been evolutionary isolated from the surrounding marine environment for more than 10,000 years since the Blue Hole formation during the last Ice Age. A total of 48 high-quality metagenome-assembled genomes (MAGs) were recovered, predominantly composed of the phyla Chloroflexota, Proteobacteria and Desulfobacterota. None of these MAGs have been classified to species level (<95% ANI), suggesting the discovery of several new microbial taxa. In particular, MAGs belonging to novel bacterial genera within the order Dehalococcoidales accounted for 20% of the macroscopic mat community. Genome-resolved metabolic analysis of this dominant microbial fraction revealed a mixotrophic lifestyle based on energy conservation via fermentation, hydrogen metabolism and anaerobic CO2 fixation through the Wood-Ljungdahl pathway. Interestingly, these bacteria showed a high proportion of ancestral genes in their genomes providing intriguing perspectives on mechanisms driving microbial evolution in this peculiar environment. Overall, our results provide new knowledge for understanding microbial life under extreme conditions in blue hole environments.},
}
@article {pmid39275913,
year = {2024},
author = {Takada, K and Nakagawa, S and Kryukov, K and Ozawa, M and Watanabe, T},
title = {Metagenomic analysis of the gut microbiota of hooded cranes (Grus monacha) on the Izumi plain in Japan.},
journal = {FEBS open bio},
volume = {},
number = {},
pages = {},
doi = {10.1002/2211-5463.13881},
pmid = {39275913},
issn = {2211-5463},
support = {//Crane Conservation by the City of Izumi/ ; //Tokyo Biochemical Research Foundation/ ; JPMJCR20H6//Core Research for Evolutional Science and Technology/ ; //2020 Tokai University School of Medicine Research Aid/ ; 22gm1610010h0001//Japan Agency for Medical Research and Development/ ; JP223fa627002h//Japan Agency for Medical Research and Development/ ; //Takeda Science Foundation/ ; 16H06429//Japan Society for the Promotion of Science/ ; 16H06434//Japan Society for the Promotion of Science/ ; 16K21723//Japan Society for the Promotion of Science/ ; 19H04843//Japan Society for the Promotion of Science/ ; 19fk0108171//Japan Society for the Promotion of Science/ ; 21J01036//Japan Society for the Promotion of Science/ ; 22K15469//Japan Society for the Promotion of Science/ ; JP19fk0108113//Japan Society for the Promotion of Science/ ; JP22H02521//Japan Society for the Promotion of Science/ ; },
abstract = {Recent advances in DNA sequencing technology have dramatically improved our understanding of the gut microbiota of various animal species. However, research on the gut microbiota of birds lags behind that of many other vertebrates, and information about the gut microbiota of wild birds such as migratory waterfowl is particularly lacking. Because the ecology of migratory waterfowl (e.g., lifestyle, diet, physiological characteristics) differs from that of other birds, the gut microbiota of migratory waterfowl likely also differs, but much is still unknown. The hooded crane (Grus monacha) is an important representative migratory waterbird species and is listed as endangered on the International Union for Conservation of Nature and Natural Resources Red List of Threatened Species. In this study, we analyzed the bacterial and viral microbiota in the gut of hooded cranes by using deep sequencing data from fecal samples of hooded cranes that winter on the Izumi plain in Japan, and found that Cetobacterium, Clupeiformes, and Pbunavirus were clearly present in the fecal samples of hooded cranes. These findings advance our understanding of the ecology of hooded cranes.},
}
@article {pmid39275258,
year = {2024},
author = {Wang, M and Chen, Y and Song, AX and Weng, X and Meng, Y and Lin, J and Mao, YH},
title = {The Combination of Exercise and Konjac Glucomannan More Effectively Prevents Antibiotics-Induced Dysbiosis in Mice Compared with Singular Intervention.},
journal = {Nutrients},
volume = {16},
number = {17},
pages = {},
pmid = {39275258},
issn = {2072-6643},
support = {2023A1515010004//Guangdong Basic and Applied Basic Research Foundation/ ; 2023ZDZX2035//Special Funds in Key Areas of Guangdong Provincial Department of Education/ ; S202410585045//The College Students Innovation and Entrepreneurship Training Program/ ; 202410585015//The College Students Innovation and Entrepreneurship Training Program/ ; 82003434//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Mannans/pharmacology ; *Dysbiosis/prevention &amp; control/chemically induced ; *Mice, Inbred C57BL ; *Anti-Bacterial Agents/pharmacology/adverse effects ; *Gastrointestinal Microbiome/drug effects ; *Physical Conditioning, Animal ; Mice ; Male ; Combined Modality Therapy ; },
abstract = {Our previous studies have demonstrated that konjac glucomannan (KGM) can prevent dysbiosis induced by antibiotics. While exercise may also impact the gut microbiome, there are limited studies reporting its protective effect on antibiotic-induced dysbiosis. Therefore, this study investigated the preventive and regulatory effects of a combination of 6-week exercise and KGM intervention on antibiotic-induced dysbiosis in C57BL/6J mice compared with a single intervention. The results showed that combined exercise and KGM intervention could restore the changes in the relative abundance of Bacteroides (3.73% with CTL versus 14.23% with ATBX versus 4.46% with EK) and Prevotellaceae_Prevotella (0.33% with CTL versus 0.00% with ATBX versus 0.30% with EK) induced by antibiotics (p < 0.05), and minimized the Bray-Curtis distance induced by antibiotics (0.55 with CTL versus 0.81 with ATBX versus 0.80 with EXC versus 0.83 with KGM versus 0.75 with EK). Compared with the combined intervention, exercise intervention also produced a certain level of recovery effects; the relative abundance of Rikenellaceae (1.96% with CTL versus 0.09% with ATBX versus 0.49% with EXC) was restored, while KGM supplementation showed the best preventive effect. In addition, the combination of exercise and KGM significantly enriched microbial purine metabolic pathways (p < 0.05). These findings indicate that combining exercise with KGM could be a promising approach to reducing the side effects of antibiotics on the gut microbiome.},
}
@article {pmid39274545,
year = {2024},
author = {Dera, N and Żeber-Lubecka, N and Ciebiera, M and Kosińska-Kaczyńska, K and Szymusik, I and Massalska, D and Dera, K and Bubień, K},
title = {Intrauterine Shaping of Fetal Microbiota.},
journal = {Journal of clinical medicine},
volume = {13},
number = {17},
pages = {},
pmid = {39274545},
issn = {2077-0383},
abstract = {Mechanisms resulting from the physiological immaturity of the digestive system in children delivered before 32 weeks of gestation and, in particular, different interactions between the microbiome and the body have not been fully elucidated yet. Next-generation sequencing methods demonstrated the presence of bacterial DNA in the placenta and amniotic fluid, which may reflect bacterial populations that initiate intestinal colonization in utero. Numerous studies confirmed the hypothesis stating that intestinal bacteria played an important role in the pathogenesis of necrotizing enterocolitis (NEC) early- and late-onset neonatal sepsis (EONS and LONS). The model and scale of disorders within the intestinal microbiome are the subject of active research in premature infants. Neonatal meconium was primarily used as an indicator defining the environment in utero, as it is formed before birth. Metagenomic results and previous data from microbiological bacterial cultures showed a correlation between the time from birth to sample collection and the detection of bacteria in the neonatal meconium. Therefore, it may be determined that the colonization of the newborn's intestines is influenced by numerous factors, which may be divided into prenatal, perinatal, and postnatal, with particular emphasis put on the mode of delivery and contact with the parent immediately after birth. Background: The aim of this review was to collect available data on the intrauterine shaping of the fetal microbiota. Methods: On 13 March 2024, the available literature in the PubMed National Library of Medicine search engine was reviewed using the following selected keywords: "placental microbiome", "intestinal bacteria in newborns and premature infants", and "intrauterine microbiota". Results: After reviewing the available articles and abstracts and an in-depth analysis of their content, over 100 articles were selected for detailed elaboration. We focused on the origin of microorganisms shaping the microbiota of newborns. We also described the types of bacteria that made up the intrauterine microbiota and the intestinal microbiota of newborns. Conclusions: The data presented in the review on the microbiome of both term newborns and those with a body weight below 1200 g indicate a possible intrauterine colonization of the fetus depending on the duration of pregnancy. The colonization occurs both via the vaginal and intestinal route (hematogenous route). However, there are differences in the demonstrated representatives of various types of bacteria, phyla Firmicutes and Actinobacteria in particular, taking account of the distribution in their abundance in the individual groups of pregnancy duration. Simultaneously, the distribution of the phyla Actinobacteria and Proteobacteria is consistent. Considering the duration of pregnancy, it may also be concluded that the bacterial flora of vaginal origin dominates in preterm newborns, while the flora of intestinal origin dominates in term newborns. This might explain the role of bacterial and infectious factors in inducing premature birth with the rupture of fetal membranes.},
}
@article {pmid39273435,
year = {2024},
author = {Di Chiano, M and Sallustio, F and Fiocco, D and Rocchetti, MT and Spano, G and Pontrelli, P and Moschetta, A and Gesualdo, L and Gadaleta, RM and Gallone, A},
title = {Psychobiotic Properties of Lactiplantibacillus plantarum in Neurodegenerative Diseases.},
journal = {International journal of molecular sciences},
volume = {25},
number = {17},
pages = {},
pmid = {39273435},
issn = {1422-0067},
support = {1062//PON "RICERCA E INNOVAZIONE" 2014-2020-Innovazione/ ; Call for tender No. 341 of 15 March 2022 of Italian Ministry of University and Research funded by the European Union - Next Generation EU//National Recovery and Resilience Plan (NRRP)/ ; Concession Decree No. 1550 of 11 October 2022 adopted by the Italian Ministry of University and Research, CUP D93C22000890001//Italian Ministry of University and Research, CUP D93C22000890001/ ; Codice progetto n. 2022H9MPZ5//MIUR- PRIN Progetti di Ricerca di Rilevante Interesse Nazionale 2022/ ; Id. 23239//AIRC IG 2019/ ; Call for tender No. 3138 of 16/12/2021 of Italian Ministry of University and Research funded by the European Union//National Recovery and Resilience Plan (NRRP)/ ; Project code: CN00000041, CUP H93C22000430007//NextGenerationEU/ ; PNRR-MR1-2022-12376395//European Union - Next Generation EU - PNRR M6C2/ ; "POFACS" - ARS01_00640 -", D.D. 1211/2020 and 1104/2021//Italian Ministry of University and Research (MIUR)/ ; PRA-HE 2021//University of Foggia/ ; },
mesh = {Humans ; *Neurodegenerative Diseases/microbiology/metabolism ; *Gastrointestinal Microbiome ; *Probiotics/therapeutic use ; Dysbiosis/microbiology ; Brain-Gut Axis ; Animals ; },
abstract = {Neurodegenerative disorders are the main cause of cognitive and physical disabilities, affect millions of people worldwide, and their incidence is on the rise. Emerging evidence pinpoints a disturbance of the communication of the gut-brain axis, and in particular to gut microbial dysbiosis, as one of the contributors to the pathogenesis of these diseases. In fact, dysbiosis has been associated with neuro-inflammatory processes, hyperactivation of the neuronal immune system, impaired cognitive functions, aging, depression, sleeping disorders, and anxiety. With the rapid advance in metagenomics, metabolomics, and big data analysis, together with a multidisciplinary approach, a new horizon has just emerged in the fields of translational neurodegenerative disease. In fact, recent studies focusing on taxonomic profiling and leaky gut in the pathogenesis of neurodegenerative disorders are not only shedding light on an overlooked field but are also creating opportunities for biomarker discovery and development of new therapeutic and adjuvant strategies to treat these disorders. Lactiplantibacillus plantarum (LBP) strains are emerging as promising psychobiotics for the treatment of these diseases. In fact, LBP strains are able to promote eubiosis, increase the enrichment of bacteria producing beneficial metabolites such as short-chain fatty acids, boost the production of neurotransmitters, and support the homeostasis of the gut-brain axis. In this review, we summarize the current knowledge on the role of the gut microbiota in the pathogenesis of neurodegenerative disorders with a particular focus on the benefits of LBP strains in Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, autism, anxiety, and depression.},
}
@article {pmid39273328,
year = {2024},
author = {Zhu, N and Qian, Y and Song, L and Yu, Q and Sheng, H and Li, Y and Zhu, X},
title = {Regulating Leaf Photosynthesis and Soil Microorganisms through Controlled-Release Nitrogen Fertilizer Can Effectively Alleviate the Stress of Elevated Ambient Ozone on Winter Wheat.},
journal = {International journal of molecular sciences},
volume = {25},
number = {17},
pages = {},
pmid = {39273328},
issn = {1422-0067},
support = {BE2022312//Special Technology Innovation Fund of Carbon Neutrality in Jiangsu Province/ ; },
mesh = {*Fertilizers ; *Triticum/growth &amp; development/metabolism/microbiology/drug effects ; *Photosynthesis/drug effects ; *Soil Microbiology ; *Plant Leaves/drug effects/metabolism ; *Nitrogen/metabolism ; *Ozone/pharmacology ; Stress, Physiological ; Soil/chemistry ; Bacteria/drug effects/metabolism/genetics ; },
abstract = {The mitigation mechanisms of a kind of controlled-release nitrogen fertilizer (sulfur-coated controlled-release nitrogen fertilizer, SCNF) in response to O3 stress on a winter wheat (Triticum aestivum L.) variety (Nongmai-88) were studied in crop physiology and soil biology through the ozone-free-air controlled enrichment (O3-FACE) simulation platform and soil microbial metagenomics. The results showed that SCNF could not delay the O3-induced leaf senescence of winter wheat but could enhance the leaf size and photosynthetic function of flag leaves, increase the accumulation of nutrient elements, and lay the foundation for yield by regulating the release rate of nitrogen (N). By regulating the soil environment, SCNF could maintain the diversity and stability of soil bacterial and archaeal communities, but there was no obvious interaction with the soil fungal community. By alleviating the inhibition effects of O3 on N-cycling-related genes (ko00910) of soil microorganisms, SCNF improved the activities of related enzymes and might have great potential in improving soil N retention. The results demonstrated the ability of SCNF to improve leaf photosynthetic function and increase crop yield under O3-polluted conditions in the farmland ecosystem, which may become an effective nitrogen fertilizer management measure to cope with the elevated ambient O3 and achieve sustainable production.},
}
@article {pmid39273112,
year = {2024},
author = {Druker, S and Sicsic, R and Ravid, S and Scheinin, S and Raz, T},
title = {Reproductive Tract Microbial Transitions from Late Gestation to Early Postpartum Using 16S rRNA Metagenetic Profiling in First-Pregnancy Heifers.},
journal = {International journal of molecular sciences},
volume = {25},
number = {17},
pages = {},
pmid = {39273112},
issn = {1422-0067},
mesh = {Female ; Animals ; Pregnancy ; *RNA, Ribosomal, 16S/genetics ; Cattle ; *Postpartum Period ; *Vagina/microbiology ; *Microbiota/genetics ; *Uterus/microbiology ; Bacteria/classification/genetics/isolation &amp; purification ; Metagenomics/methods ; Metagenome ; },
abstract = {Studies in recent years indicate that reproductive tract microbial communities are crucial for shaping mammals' health and reproductive outcomes. Following parturition, uterine bacterial contamination often occurs due to the open cervix, which may lead to postpartum uterine inflammatory diseases, especially in primiparous individuals. However, investigations into spatio-temporal microbial transitions in the reproductive tract of primigravid females remain limited. Our objective was to describe and compare the microbial community compositions in the vagina at late gestation and in the vagina and uterus at early postpartum in first-pregnancy heifers. Three swab samples were collected from 33 first-pregnancy Holstein Friesian heifers: one vaginal sample at gestation day 258 ± 4, and vaginal and uterine samples at postpartum day 7 ± 2. Each sample underwent 16S rRNA V4 region metagenetic analysis via Illumina MiSeq, with bioinformatics following Mothur MiSeq SOP. The reproductive tract bacterial communities were assigned to 1255 genus-level OTUs across 30 phyla. Dominant phyla, accounting for approximately 90% of the communities, included Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, and Fusobacteria. However, the results revealed distinct shifts in microbial composition between the prepartum vagina (Vag-pre), postpartum vagina (Vag-post), and postpartum uterus (Utr-post). The Vag-pre and Utr-post microbial profiles were the most distinct. The Utr-post group had lower relative abundances of Proteobacteria but higher abundances of Bacteroidetes, Fusobacteria, and Tenericutes compared to Vag-pre, while Vag-post displayed intermediate values for these phyla, suggesting a transitional profile. Additionally, the Utr-post group exhibited lower bacterial richness and diversity compared to both Vag-pre and Vag-post. The unsupervised probabilistic Dirichlet Multinomial Mixtures model identified two distinct community types: most Vag-pre samples clustered into one type and Utr-post samples into another, while Vag-post samples were distributed evenly between the two. LEfSe analysis revealed distinct microbial profiles at the genus level. Overall, specific microbial markers were associated with anatomical and temporal transitions, revealing a dynamic microbial landscape during the first pregnancy and parturition. These differences highlight the complexity of these ecosystems and open new avenues for research in reproductive biology and microbial ecology.},
}
@article {pmid39271469,
year = {2024},
author = {Ciuchcinski, K and Stokke, R and Steen, IH and Dziewit, L},
title = {Landscape of the Metaplasmidome of Deep-Sea Hydrothermal Vents located at Arctic Mid-Ocean Ridges in the Norwegian-Greenland Sea - Ecological Insights from Comparative Analysis of Plasmid Identification Tools.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiae124},
pmid = {39271469},
issn = {1574-6941},
abstract = {Plasmids are one of the key drivers of microbial adaptation and evolution. However, their diversity and role in adaptation, especially in extreme environments, remains largely unexplored. In this study, we aimed to identify, characterize and compare plasmid sequences originating from samples collected from deep-sea hydrothermal vents located in Arctic Mid-Ocean Ridges. To achieve this, we employed, and benchmarked three recently developed plasmid identification tools - PlasX, GeNomad and PLASMe - on metagenomic data from this unique ecosystem. To date, this is the first direct comparison of these computational methods in the context of data from extreme environments. Upon recovery of plasmid contigs, we performed a multi-approach analysis, focusing on identifying taxonomic and functional biases within datasets originating from each tool. Next, we implemented a majority voting system to identify high-confidence plasmid contigs, enhancing the reliability of our findings. By analyzing the consensus plasmid sequences, we gained insights into their diversity, ecological roles, and adaptive significance. Within the high-confidence sequences, we identified a high abundance of Pseudomonadota and Campylobacterota, as well as multiple toxin-antitoxin systems. Our findings ensure a deeper understanding of how plasmids contribute to shaping microbial communities living under extreme conditions of hydrothermal vents, potentially uncovering novel adaptive mechanisms.},
}
@article {pmid39271424,
year = {2024},
author = {Bokulich, NA and Robeson, MS},
title = {Bioinformatics challenges for profiling the microbiome in cancer: pitfalls and opportunities.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2024.08.011},
pmid = {39271424},
issn = {1878-4380},
abstract = {Increasing evidence suggests that the human microbiome plays an important role in cancer risk and treatment. Untargeted 'omics' techniques have accelerated research into microbiome-cancer interactions, supporting the discovery of novel associations and mechanisms. However, these techniques require careful selection and use to avoid biases and other pitfalls. In this essay, we discuss selected challenges involved in the analysis of microbiome data in the context of cancer, including the application of machine learning (ML). We focus on DNA sequencing-based (e.g., metagenomics) methods, but many of the pitfalls and opportunities generalize to other omics technologies as well. We advocate for extended training opportunities, community standards, and best practices for sharing data and code to advance transparency and reproducibility in cancer microbiome research.},
}
@article {pmid39271095,
year = {2024},
author = {do Socorro Foro Ramos, E and Barbosa, MRF and Villanova, F and Silva, RLO and Garcia, SC and Mendes-Correa, MC and Pandey, RP and Luchs, A and Sato, MIZ and da Costa, AC and Leal, E},
title = {Novel members of the order Picornavirales identified in freshwater from Guarapiranga reservoir in São Paulo.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {124},
number = {},
pages = {105668},
doi = {10.1016/j.meegid.2024.105668},
pmid = {39271095},
issn = {1567-7257},
mesh = {Brazil ; *Fresh Water/virology ; *Phylogeny ; Metagenomics/methods ; Genome, Viral ; Picornaviridae/genetics/classification/isolation &amp; purification ; },
abstract = {The global challenge of water resource availability is exacerbated by anthropogenic influences that promote the emergence of pollutants. Among these pollutants are microbiological agents, including viruses, which are ubiquitous in the biosphere and play a pivotal role in both ecological balance and the occurrence of diseases in animals and plants. Consequently, monitoring viruses in water sources becomes indispensable for the establishment of effective prevention, promotion, and control strategies. Within this context, the study focuses on the identification of novel viruses belonging to the Picornavirales order in freshwater from the Guarapiranga Reservoir in the state of São Paulo, Brazil. The samples were subjected to viral metagenomics. Our analysis led to the characterization of four distinct sequences (GinkV-05, AquaV_10, MarV_14, and MarV_64), which exhibited significant divergence compared to other members of the Picornavirales order. This remarkable diversity prompted the identification of a potential new genus within the Marnaviridae family, tentatively named Ginkgonavirus. Additionally, we characterized four sequences in a very distinct clade and propose the recognition of a novel family (named Aquaviridae) within the Picornavirales order. Our findings contribute valuable insights into the previously uncharted diversity of Picornavirales present in water sources, shedding light on an important facet of viral ecology and evolution in aquatic environments.},
}
@article {pmid39271075,
year = {2024},
author = {Xu, X and Chen, H and Du, L and Deng, C and Ma, R and Li, B and Li, J and Liu, S and Karthikeyan, R and Chen, Q and Sun, W},
title = {Distribution and drivers of co-hosts of antibiotic and metal(loid) resistance genes in the fresh-brackish-saline groundwater.},
journal = {Chemosphere},
volume = {365},
number = {},
pages = {143332},
doi = {10.1016/j.chemosphere.2024.143332},
pmid = {39271075},
issn = {1879-1298},
abstract = {Groundwater is an essential source of drinking water and agricultural irrigation water, and its protection has become a global goal for public health. However, knowledge about heavy metal(loid) resistance genes (MRGs) in groundwater and the potential co-selection of antibiotic resistance genes (ARGs) have seldom been developed. Here, during the wet and dry seasons, we collected 66 groundwater samples (total dissolved solids = 93.9-9530 mg/L) adjacent to Baiyangdian Lake in Northern China, which presented the few metal(loid) and antibiotic contamination. We identified 160 MRGs whose composition exhibited significant seasonal variation, and dissolved metal(loid)s (particularly Ba) played a determinative role in promoting the MRGs proliferation though with relatively low concentrations, suggesting the relatively vulnerable groundwater ecosystems. Moreover, 27.4% of MRG-carrying metagenome-assembled genomes (MAGs) simultaneously carried ARGs, with the most frequently detected MRG types of Cu, Hg, and As, and ARG types of multidrug and bacitracin. Physicochemical variables, variables related to total dissolved solids, metal(loid)s, and antibiotics synthetically shaped the variation of MRG-ARG hosts in groundwater. We found that the increase of MRG-ARG hosts was critically responsible for the spread of MRGs and ARGs in groundwater. Our findings revealed the widespread co-occurrence of MRGs and ARGs in few-contaminated groundwater and highlighted the crucial roles of salinity in their propagation and transmission.},
}
@article {pmid39270978,
year = {2024},
author = {Fang, Z and Zang, Q and Chen, J and Li, Z and Yang, D and Wu, C and Yang, H and Guo, N},
title = {Whole-body mass spectrometry imaging reveals the systemic metabolic disorder and catecholamines biosynthesis alteration on heart-gut axis in heart failure rat.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2024.09.001},
pmid = {39270978},
issn = {2090-1224},
abstract = {INTRODUCTION: Heart failure (HF) is a systemic metabolic disorder disease, across multiorgan investigations advancing knowledge of progression and treatment of HF. Whole-body MSI provides spatiotemporal information of metabolites in multiorgan and is expected to be a potent tool to dig out the complex mechanism of HF.<br><br>OBJECTIVES: This study aimed at exploring the systemic metabolic disorder in multiorgan and catecholamines biosynthesis alteration on heart-gut axis after HF.<br><br>METHODS: Whole-body MSI was used to characterize metabolic disorder of the whole rat body after HF. An integrated method by MSI, LC-MS/MS and ELISA was utilized to analyze key metabolites and enzymes on heart, small intestine, cecum and colon tissues of rat. Gut microbiota dysbiosis was investigated by 16S rDNA sequencing and metagenomic sequencing. Validation experiments and in vitro experiments were performed to verify the effect of catecholamines biosynthesis alteration on heart-gut axis after HF.<br><br>RESULTS: Whole-body MSI exhibited varieties of metabolites alteration in multiple organs. Remarkably, Catecholamine biosynthesis was significantly altered in the serum, heart and intestines of rats. Furthermore, catecholamines and tyrosine hydroxylase were obviously upregulated in heart and colon tissue. Turicibacter_sanguinis was relevant to catecholamines of heart and colon. Validation experiments demonstrated excessive norepinephrine induced cardio-intestinal injury, including significantly elevating the levels of BNP, pro-BNP, LPS, DAO, and increased the abundance of Turicibacter_sanguinis. These alterations could be reversed by metoprolol treatment blocking the effect of norepinephrine. Additionally, in vitro studies demonstrated that norepinephrine promoted the growth of Turicibacter_sanguinis and Turicibacter_sanguinis could import and metabolize norepinephrine. Collectively, excessive norepinephrine exerted bidirectional effects on cardio-intestinal function to participate in the progression of HF.<br><br>CONCLUSION: Our study provides a new approach to elucidate multiorgan metabolic disorder and proposes new insights into heart-gut axis in HF development.},
}
@article {pmid39270881,
year = {2024},
author = {Bai, M and Zhou, Z and Yin, M and Wang, M and Gao, X and Zhao, J},
title = {The use of metagenomic and untargeted metabolomics in the analysis of the effects of the Lycium barbarum glycopeptide on allergic airway inflammation induced by Artemesia annua pollen.},
journal = {Journal of ethnopharmacology},
volume = {337},
number = {Pt 1},
pages = {118816},
doi = {10.1016/j.jep.2024.118816},
pmid = {39270881},
issn = {1872-7573},
abstract = {The prevalence of allergic airway inflammation (AAI) worldwide is high. Artemisia annua L. pollen is spread worldwide, and allergic diseases caused by its plant polysaccharides, which are closely related to the intestinal microbiota, have anti-inflammatory effects. Further isolation and purification of Lycium barbarum L. yielded its most effective component Lycium barbarum L. glycopeptide (LbGP), which can inhibit inflammation in animal models. However, its therapeutic effect on AAI and its mechanism of regulating the intestinal flora have not been fully investigated.<br><br>AIM OF THE STUDY: To explore LbGP in APE-induced immunological mechanisms of AAI and the interaction mechanism of the intestinal flora and metabolites.<br><br>METHODS: A mouse model of AAI generated from Artemisia annua pollen was constructed, and immunological indices related to the disease were examined. A combination of macrogenomic and metabolomic analyses was used to investigate the effects of LbGP on the gut microbial and metabolite profiles of mice with airway inflammation.<br><br>RESULTS: LbGP effectively alleviated Artemisia. annua pollen extract (APE)-induced AAI, corrected Th1/Th2 immune dysregulation, decreased Th17&#xa0;cells, increased Treg cells, and altered the composition and function of the intestinal microbiota. LbGP treatment increased the number of OdoribacterandDuncaniella in the intestines of the mice, but the numble of Alistipes and Ruminococcus decreased. Metabolite pathway enrichment analysis were used to determine the effects of taurine and hypotaurine metabolism, bile acid secretion, and pyrimidine metabolism pathways on disease.<br><br>CONCLUSION: Our results revealed significant changes in the macrogenome and metabolome following APE and LbGP intervention, revealed potential correlations between gut microbial species and metabolites, and highlighted the beneficial effects of LbGP on AAI through the modulation of the gut microbiome and host metabolism.},
}
@article {pmid39270504,
year = {2024},
author = {Deng, J and Kang, D and Zhang, Y and Chen, B and Xia, C and Yu, C and Peng, Y},
title = {Genome-resolved metagenomics reveals the nitrifiers enrichment and species succession in activated sludge under extremely low dissolved oxygen.},
journal = {Water research},
volume = {266},
number = {},
pages = {122420},
doi = {10.1016/j.watres.2024.122420},
pmid = {39270504},
issn = {1879-2448},
abstract = {Nitrification, a process carried out by aerobic microorganisms that oxidizes ammonia to nitrate via nitrite, is an indispensable step in wastewater nitrogen removal. To facilitate energy and carbon savings, applying low dissolved oxygen (DO) is suggested to shortcut the conventional biological nitrogen removal pathway, however, the impact of low DO on nitrifying communities within activated sludge is not fully understood. This study used genome-resolved metagenomics to compare nitrifying communities under extremely low- and high-DO. Two bioreactors were parallelly operated to perform nitrification and DO was respectively provided by limited gas-liquid mass transfer from the atmosphere (AN reactor, DO < 0.1 mg/L) and by sufficient aeration (AE reactor, DO > 5.0 mg/L). Low DO was thought to limit nitrifiers growth; however, we demonstrated that complete nitrification could still be achieved under the extremely low-DO conditions, but with no nitrite accumulation observed. Kinetic analysis showed that after long-term exposure to low DO, nitrifiers had a higher oxygen affinity constant and could maintain a relatively high nitrification rate, particularly at low levels of DO (<0.2 mg/L). Community-level gene analysis indicated that low DO promoted enrichment of nitrifiers (the genera Nitrosomonas and Nitrospira, increased by 2.3- to 4.3-fold), and also harbored with 2.3 to 5.3 times higher of nitrification functional genes. Moreover, 46 high-quality (>90 % completeness and <5 % contamination) with 3 most abundant medium-quality metagenome-assembled genomes (MAGs) were retrieved using binning methods. Genome-level phylogenetic analysis revealed the species succession within nitrifying populations. Surprisingly, compared to DO-rich conditions, low-DO conditions were found to efficiently suppressed the ordinary heterotrophic microorganisms (e.g., the families Anaerolineales, Phycisphaerales, and Chitinophagales), but selected for the specific candidate denitrifiers (within phylum Bacteroidota). This study provides new microbial insights to demonstrate that low-DO favors the enrichment of autotrophic nitrifiers over heterotrophs with species-level successions, which would facilitate the optimization of energy and carbon management in wastewater treatment.},
}
@article {pmid39270468,
year = {2024},
author = {Erdemir, F and Karabulut, A and Aydin, U and Guler, S and Cicek, A and Gokduman, SN and Eser, E and Birdogan, S and Kocagoz, T},
title = {Metagenomic analysis of atheroma plaques for identification of microorganisms indicates presence of Toxoplasma gondii as a possible etiological agent.},
journal = {Journal of infection and public health},
volume = {17},
number = {10},
pages = {102539},
doi = {10.1016/j.jiph.2024.102539},
pmid = {39270468},
issn = {1876-035X},
mesh = {Humans ; *Toxoplasma/genetics/isolation &amp; purification ; *Plaque, Atherosclerotic/microbiology ; *Metagenomics/methods ; Female ; Male ; Aged ; Middle Aged ; Carotid Stenosis/microbiology ; Polymerase Chain Reaction/methods ; Toxoplasmosis/parasitology/microbiology/diagnosis ; DNA, Protozoan/genetics ; Aged, 80 and over ; Whole Genome Sequencing ; Carotid Arteries ; Bacteria/isolation &amp; purification/classification/genetics ; },
abstract = {BACKGROUND: Cardiovascular diseases (CVDs) are the leading cause of death worldwide. Vital organs like the heart are affected by the occlusion of blood vessels due to atherosclerotic plaque formation. However, the role of infectious agents has always been an essential subject of investigation. This study investigated the presence of microorganisms, including nanobacteria, in atherosclerotic plaques removed from human carotid arteries by microbiological and metagenomic examination.<br><br>METHODS: Atheroma plaque samples were obtained from 20 patients with carotid artery stenosis who had atherectomy by surgery or percutaneous intervention. Nanobacteria were grown by culturing homogenates of the atheroma plaques. Whole genome sequencing was done for samples. Because of the high percentage of Toxoplasma gondii (T. gondii) DNA, PCR investigation was applied to detect T. gondii DNA in the samples.<br><br>RESULTS: A molecular analysis of nanobacteria revealed them to be made of human proteins, supporting the theory that they are not living organisms. According to sequencing results, samples showed that more than 50&#xa0;% of the metagenomic sequences belonged to Toxoplasma gondii. PCR investigation indicated that T. gondii DNA was positive in 8 (40&#xa0;%) of 20 plaques.<br><br>CONCLUSIONS: Further evidence regarding the role of T. gondii in the etiology of plaque formation may help determine the strategy for prevention and treatment of infections in preventing atheroma plaque formation in the future.},
}
@article {pmid39269181,
year = {2024},
author = {Quan, Q and Liu, J and Li, C and Ke, Z and Tan, Y},
title = {Insights into prokaryotic communities and their potential functions in biogeochemical cycles in cold seep.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0054924},
doi = {10.1128/msphere.00549-24},
pmid = {39269181},
issn = {2379-5042},
abstract = {UNLABELLED: Microorganisms are significant drivers of organic matter mineralization and are essential in marine biogeochemical cycles. However, the variations and influencing factors in prokaryotic communities from cold-seep sediments to the water column and the specific role of these microorganisms in biogeochemical cycles in the water column above cold seep remain unclear. Here, we investigated prokaryotic communities and their roles in nitrogen/sulfur cycling processes and conducted in situ dissolved organic matter (DOM) enrichment experiments to explore the effects of diverse sources of DOM on prokaryotic communities. Field investigations showed that the prokaryotic communities in the near-bottom water were more similar to those in the deep layer of the euphotic zone (44.60%) and at a depth of 400 m (50.89%) than those in the sediment (18.00%). DOM enrichment experiments revealed that adding dissolved organic nitrogen (DON) and phosphorus DOP caused a notable increase in the relative abundances of Rhodobacterales and Vibrionales, respectively. A remarkable increase was observed in the relative abundance of Alteromonadales and Pseudomonadales after the addition of dissolved organic sulfur (DOS). The metagenomic results revealed that Proteobacteria served as the keystone taxa in mediating the biogeochemical cycles of nitrogen, phosphorus, and sulfur in the Haima cold seep. This study highlights the responses of prokaryotes to DOM with different components and the microbially driven elemental cycles in cold seeps, providing a foundational reference for further studies on material energy metabolism and the coupled cycling of essential elements mediated by deep-sea microorganisms.<br><br>IMPORTANCE: Deep-sea cold seeps are among the most productive ecosystems, sustaining unique fauna and microbial communities through the release of methane and other hydrocarbons. Our study revealed that the influence of seepage fluid on the prokaryotic community in the water column is surprisingly limited, which challenges conventional views regarding the impact of seepage fluids. In addition, we identified that different DOM compositions play a crucial role in shaping the prokaryotic community composition, providing new insights into the factors driving microbial diversity in cold seeps. Furthermore, the study highlighted Proteobacteria as key and multifaceted drivers of biogeochemical cycles in cold seeps, emphasizing their significant contribution to complex interactions and processes. These findings offer a fresh perspective on the dynamics of cold-seep environments and their microbial communities, advancing our understanding of the biogeochemical functions in deep-sea environments.},
}
@article {pmid39268953,
year = {2024},
author = {Dai, Z and Lu, Q and Sun, M and Chen, H and Zhu, R and Wang, H},
title = {Identification of a Novel Parvovirus in the Arctic Wolf (Canis lupus arctos).},
journal = {Polish journal of microbiology},
volume = {73},
number = {3},
pages = {395-401},
pmid = {39268953},
issn = {2544-4646},
mesh = {Animals ; *Phylogeny ; *Genome, Viral ; *Wolves/virology ; *Open Reading Frames ; *Parvovirus/genetics/classification/isolation &amp; purification ; Capsid Proteins/genetics ; Parvoviridae Infections/virology/veterinary ; Base Composition ; China ; DNA, Viral/genetics ; },
abstract = {A novel virus, temporarily named "Arctic wolf parvovirus" (AWPV), was discovered in a pharyngeal metagenomic library derived from an Arctic wolf (Canis lupus arctos) in China. The genome sequence was assigned GenBase accession number C_AA071902.1. AWPV has a genome comprised of 4,920 base pairs with a nucleotide composition of 36.4% A, 23.4% T, 18.2% G, and 22.0% C, with a GC content of 40.2%. Its structure resembles parvoviruses, containing two open reading frames: the nonstructural (NS) region encoding replication enzymes and the structural (VP) region encoding capsid protein. Pairwise sequence comparison and phylogenetic analysis suggest AWPV may represent a novel species within the genus Protoparvovirus. This discovery enhances our understanding of mammalian virus ecology and potential future infectious diseases.},
}
@article {pmid39268488,
year = {2024},
author = {Hu, L and Huang, X and Yee, NH and Meng, H and Jiang, L and Liang, L and Chen, X},
title = {Pythium insidiosum: an emerging pathogen that is easily misdiagnosed and given treatment as a fungus.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1430032},
pmid = {39268488},
issn = {2235-2988},
mesh = {*Pythium/isolation &amp; purification/drug effects/genetics ; Humans ; *Pythiosis/diagnosis/microbiology/drug therapy ; *Antifungal Agents/pharmacology/therapeutic use ; *Microbial Sensitivity Tests ; Male ; Diagnostic Errors ; Communicable Diseases, Emerging/microbiology/diagnosis/drug therapy ; Keratitis/microbiology/diagnosis/drug therapy ; Middle Aged ; High-Throughput Nucleotide Sequencing ; Female ; Aged ; },
abstract = {BACKGROUND: Pythium insidiosum (P. insidiosum) is the causative agent of pythiosis, an infectious disease with a high morbidity and fatality rate. Pythiosis cases have increased dramatically during the past ten years, particularly in tropical and subtropical areas. Sadly, microbiologists and medical professionals know very little about pythiosis, and the disease is frequently challenging to identify. It is frequently misdiagnosed as a fungal infection.<br><br>METHODS: We report two cases of pythiosis, one was Pythium keratitis, the other was cutaneous pythiosis. The patient with corneal infection had no underlying disease, while the patient with cutaneous pythiosis had a history of liver cirrhosis, diabetes, and psoriasis. The corneal sample and subcutaneous pus were sent for metagenomic Next-Generation Sequencing (mNGS). To further diagnose the isolated strain, P. insidiosum zoospores were induced to produce by co-incubation with sterile grass leaves in sterile pond water. Their zoospores were used as an inoculum for drug susceptibility testing by disk diffusion and broth microdilution method.<br><br>RESULTS: The mNGS of two cases were reported as P. insidiosum. Zoospores were produced after incubation 48h. The zoospores were collected for drug susceptibility assay. All antifungal drugs, antibacterial drugs of &#x3b2;-Lactams, vancomycin, levofloxacin, ciprofloxacin, gentamicin, trimethoprim-sulfamethoxazole, clindamycin have no inhibitory activity against P. insidiosum in vitro. Minocycline, tigecycline, linezolid, erythromycin and azithromycin have significant in vitro activity against P. insidiosum. Based on the susceptibility results, the drug was changed from itraconazole to linezolid and minocycline, along with multiple debridements and drainage for cutaneous pythiosis. The patient was discharged after 24 days of treatment.<br><br>CONCLUSIONS: Early and accurate identification, combined with aggressive surgical debridement and appropriate drug therapy, can greatly improve patient managements. Conventional culture and zoospore induction remain gold standard for diagnosis; however, DNA-based method should be performed simultaneously. The drug susceptibility testing provides profound effects on proper drug selection against P. insidiosum.},
}
@article {pmid39268238,
year = {2024},
author = {Wang, J and Su, C and Qian, M and Wang, X and Chen, C and Liu, Y and Liu, W and Xiang, Z and Xu, B},
title = {Subchronic toxic effects of bisphenol A on the gut-liver-hormone axis in rats via intestinal flora and metabolism.},
journal = {Frontiers in endocrinology},
volume = {15},
number = {},
pages = {1415216},
pmid = {39268238},
issn = {1664-2392},
mesh = {Animals ; *Phenols/toxicity ; Male ; Female ; Rats ; *Gastrointestinal Microbiome/drug effects ; *Benzhydryl Compounds/toxicity ; *Liver/drug effects/metabolism/pathology ; *Endocrine Disruptors/toxicity ; Rats, Sprague-Dawley ; Hormones/blood ; },
abstract = {BACKGROUND: Bisphenol A (BPA), a characteristic endocrine disruptor, is a substance that seriously interferes with the human endocrine system and causes reproductive disorders and developmental abnormalities. However, its toxic effects on the gut-liver-hormone axis are still unclear.<br><br>METHOD: Male and female rats were exposed to BPA (300 mg/kg) by oral gavage for 60 consecutive days. H&amp;E staining was used for histopathological evaluation, and the serum biochemical indexes were determined using an automatic analyzer. The 16S rRNA gene sequencing was used to detect the intestinal microbial diversity, and the GC-MS was used to analyze the contents of short-chain fatty acids (SCFAs) in colon contents. UPLC-QTOF MS was used to analyze the related metabolites. The ELISA method was used to assess the levels of serum inflammatory factors.<br><br>RESULTS: Histopathological analysis indicated that the liver, heart, and testis were affected by BPA. There was a significant effect on alanine aminotransferase (ALT), triglyceride (TG), total cholesterol (TC), and low-density lipoprotein (LDL) in the male-BPA group (P < 0.05), and globulin (GLB), indirect bilirubin (IBIL), alkaline phosphatase (ALP), ALT, TG, TC, high-density lipoprotein (HDL), and creatinine (Cr) in the female-BPA group (P < 0.05). Metagenomics (16S rRNA gene sequencing) analysis indicated that BPA reduced the diversity and changed the composition of gut microbiota in rats significantly. Compared with the control and blank groups, the contents of caproic acid, isobutyric acid, isovaleric acid, and propanoic acid in the colon contents decreased in the male-BPA group (P < 0.05), and caproic acid, isobutyric acid, isovaleric acid, and valeric acid in the colon contents decreased in the female-BPA group (P < 0.05). Metabolomic analysis of the serum indicated that BPA could regulate bile acid levels, especially ursodeoxycholic acid (UDCA) and its conjugated forms. The contents of amino acids, hormones, and lipids were also significantly affected after exposure to BPA. The increase in interleukin-6 (IL-6), interleukin-23 (IL-23), and transforming growth factor-&#x3b2; (TGF-&#x3b2;) in the serum of the male-BPA group suggests that BPA exposure affects the immune system.<br><br>CONCLUSION: BPA exposure will cause toxicity to rats via disrupting the gut-liver-hormone axis.},
}
@article {pmid39268134,
year = {2024},
author = {Liu, X and Zhao, Q and He, X and Min, J and Yao, RSY and Chen, Z and Ma, J and Hu, W and Huang, J and Wan, H and Guo, Y and Zhou, M},
title = {Clinical characteristics and microbial signatures in the lower airways of diabetic and nondiabetic patients with pneumonia.},
journal = {Journal of thoracic disease},
volume = {16},
number = {8},
pages = {5262-5273},
pmid = {39268134},
issn = {2072-1439},
abstract = {BACKGROUND: The microbial signatures in diabetes with pneumonia and the risk factors of severe pneumonia (SP) in diabetic patients are not clear. Our study explored microbial signatures and the association between clinical characteristics and SP then constructed a risk model to find effective biomarkers for predicting pneumonia severity.<br><br>METHODS: Our study was conducted among 273 patients with pneumonia diagnosed and treated in our hospital from January 2018 to May 2021. Bronchoalveolar lavage fluid (BALF) samples and clinical data were collected. Metagenomic sequencing was applied after extracting the DNA from samples. Appropriate statistical methods were used to compare the microbial signatures and clinical characteristics in patients with or without diabetes mellitus (DM).<br><br>RESULTS: In total, sixty-one pneumonia patients with diabetes and 212 pneumonia patients without diabetes were included. Sixty-six differential microorganisms were found to be associated with SP in diabetic patients. Some microbes correlated with clinical indicators of SP. The prediction model for SP was established and the receiver operating characteristic (ROC) curve demonstrated its accuracy, with the sensitivity and specificity of 0.82 and 0.91, respectively.<br><br>CONCLUSIONS: Some microorganisms affect the severity of pneumonia. We identified the microbial signatures in the lower airways and the association between clinical characteristics and SP. The predictive model was more accurate in predicting SP by combining microbiological indicators and clinical characteristics, which might be beneficial to the early identification and management of patients with SP.},
}
@article {pmid39267171,
year = {2024},
author = {Gandasegui, J and Fleitas, PE and Petrone, P and Grau-Pujol, B and Novela, V and Rubio, E and Muchisse, O and Cossa, A and Jamine, JC and Sacoor, C and Brienen, EAT and van Lieshout, L and Muñoz, J and Casals-Pascual, C},
title = {Baseline gut microbiota diversity and composition and albendazole efficacy in hookworm-infected individuals.},
journal = {Parasites &amp; vectors},
volume = {17},
number = {1},
pages = {387},
pmid = {39267171},
issn = {1756-3305},
mesh = {*Albendazole/therapeutic use/pharmacology/administration &amp; dosage ; Humans ; *Gastrointestinal Microbiome/drug effects/genetics ; *Anthelmintics/therapeutic use/administration &amp; dosage ; *Hookworm Infections/drug therapy ; *Feces/parasitology/microbiology ; Female ; Male ; RNA, Ribosomal, 16S/genetics ; Adult ; Treatment Outcome ; Animals ; Young Adult ; Middle Aged ; Ancylostomatoidea/drug effects/genetics ; Adolescent ; Child ; },
abstract = {Soil-transmitted helminth (STH) infections account for a significant global health burden, necessitating mass drug administration with benzimidazole-class anthelmintics, such as albendazole (ALB), for morbidity control. However, ALB efficacy shows substantial variability, presenting challenges for achieving consistent treatment outcomes. We have explored the potential impact of the baseline gut microbiota on ALB efficacy in hookworm-infected individuals through microbiota profiling and machine learning (ML) techniques. Our investigation included 89 stool samples collected from hookworm-infected individuals that were analyzed by microscopy and quantitative PCR (qPCR). Of these, 44 were negative by microscopy for STH infection using the Kato-Katz method and qPCR 21 days after treatment, which entails a cure rate of 49.4%. Microbiota characterization was based on amplicon sequencing of the V3-V4 16S ribosomal RNA gene region. Alpha and beta diversity analyses revealed no significant differences between participants who were cured and those who were not cured, suggesting that baseline microbiota diversity does not influence ALB treatment outcomes. Furthermore, differential abundance analysis at the phylum, family and genus levels yielded no statistically significant associations between bacterial communities and ALB efficacy. Utilizing supervised ML models failed to predict treatment response accurately. Our investigation did not provide conclusive insights into the relationship between gut microbiota and ALB efficacy. However, the results highlight the need for future research to incorporate longitudinal studies that monitor changes in the gut microbiota related to the infection and the cure with ALB, as well as functional metagenomics to better understand the interaction of the microbiome with the drug, and its role, if there is any, in modulating anthelmintic treatment outcomes in STH infections. Interdisciplinary approaches integrating microbiology, pharmacology, genetics and data science will be pivotal in advancing our understanding of STH infections and optimizing treatment strategies globally.},
}
@article {pmid39267108,
year = {2024},
author = {Zheng, YR and Chen, XH and Chen, Q and Cao, H},
title = {Comparison of targeted next-generation sequencing and metagenomic next-generation sequencing in the identification of pathogens in pneumonia after congenital heart surgery: a comparative diagnostic accuracy study.},
journal = {Italian journal of pediatrics},
volume = {50},
number = {1},
pages = {174},
pmid = {39267108},
issn = {1824-7288},
mesh = {Humans ; Retrospective Studies ; *High-Throughput Nucleotide Sequencing ; Male ; Female ; *Heart Defects, Congenital/surgery ; Infant ; *Metagenomics/methods ; *Cardiac Surgical Procedures/adverse effects ; Postoperative Complications/diagnosis ; Infant, Newborn ; Pneumonia/diagnosis/microbiology ; Sensitivity and Specificity ; },
abstract = {BACKGROUND: This study aimed to compare targeted next-generation sequencing (tNGS) with metagenomic next-generation sequencing (mNGS) for pathogen detection in infants with severe postoperative pneumonia after congenital heart surgery.<br><br>METHODS: We conducted a retrospective observational study using data from the electronic medical record system of infants who developed severe pneumonia after surgery for congenital heart disease from August 2021 to August 2022. Infants were divided into tNGS and mNGS groups based on the pathogen detection methods. The primary outcome was the efficiency of pathogen detection, and the secondary outcomes were the timeliness and cost of each method.<br><br>RESULTS: In the study, 91 infants were included, with tNGS detecting pathogens in 84.6% (77/91) and mNGS in 81.3% (74/91) of cases (P&#x2009;=&#x2009;0.55). No significant differences were found in sensitivity, specificity, PPA, and NPA between the two methods (P&#x2009;>&#x2009;0.05). tNGS identified five strains with resistance genes, while mNGS detected one strain. Furthermore, tNGS had a faster detection time (12 vs. 24&#xa0;h) and lower cost ($150 vs. $500) compared to mNGS.<br><br>CONCLUSION: tNGS offers similar sensitivity to mNGS but with greater efficiency and cost-effectiveness, making it a promising approach for respiratory pathogen detection.},
}
@article {pmid39267031,
year = {2024},
author = {Liu, H and Ran, Q and Ma, J and Zhang, J and Tan, N and Xi, L and Li, X and Zhang, J and Lu, S},
title = {Retrospective clinical and microbiologic analysis of metagenomic next-generation sequencing in the microbiological diagnosis of cutaneous infectious granulomas.},
journal = {Annals of clinical microbiology and antimicrobials},
volume = {23},
number = {1},
pages = {84},
pmid = {39267031},
issn = {1476-0711},
support = {82172289//National Natural Science Foundation of China/ ; 202201020345//Guangzhou Municipal Science and Technology Project/ ; },
mesh = {Humans ; Retrospective Studies ; Male ; Female ; Middle Aged ; Adult ; *Granuloma/microbiology/diagnosis ; *High-Throughput Nucleotide Sequencing/methods ; Bacteria/isolation &amp; purification/genetics/classification ; Aged ; Sensitivity and Specificity ; Fungi/isolation &amp; purification/genetics/classification ; Young Adult ; Metagenomics/methods ; Skin Diseases, Infectious/diagnosis/microbiology ; Adolescent ; Skin/microbiology/pathology ; Child ; },
abstract = {BACKGROUND: Cutaneous infectious granulomas (CIG) are localized and chronic skin infection caused by a variety of pathogens such as protozoans, bacteria, worms, viruses and fungi. The diagnosis of CIG is difficult because microbiological examination shows low sensitivity and the histomorphological findings of CIG caused by different pathogens are commonly difficult to be distinguished.<br><br>OBJECTIVE: The objective of this study is to explore the application of mNGS in tissue sample testing for CIG cases, and to compare mNGS with traditional microbiological methods by evaluating sensitivity and specificity.<br><br>METHODS: We conducted a retrospective study at the Department of Dermatology of Sun Yat-sen Memorial Hospital, Sun Yat-sen University from January 1st, 2020, to May 31st, 2024. Specimens from CIG patients with a clinical presentation of cutaneous infection that was supported by histological examination were retrospectively enrolled. Specimens were delivered to be tested for microbiological examinations and mNGS.<br><br>RESULTS: Our data show that mNGS detected Non-tuberculosis mycobacteria, Mycobacterium tuberculosis, fungi and bacteria in CIG. Compared to culture, mNGS showed a higher positive rate (80.77% vs. 57.7%) with high sensitivity rate (100%) and negative predictive value (100%). In addition, mNGS can detect more pathogens in one sample and can be used to detect variable samples including the samples of paraffin-embedded tissue with shorter detective time. Of the 21 patients who showed clinical improvement within a 30-day follow-up, eighteen had their treatments adjusted, including fifteen who continued treatment based on the results of mNGS.<br><br>CONCLUSIONS: mNGS could provide a potentially rapid and effective alternative detection method for diagnosis of cutaneous infectious granulomas and mNGS results may affect the clinical prognosis resulting from enabling the patients to initiate timely treatment.},
}
@article {pmid39266944,
year = {2024},
author = {Meirelles, PM and Viana, PAB and Tschoeke, DA and de Moraes, L and Santos, LA and Barral-Netto, M and Khouri, R and Ramos, PIP},
title = {Optimizing next-generation sequencing efficiency in clinical settings: analysis of read length impact on cost and performance.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {856},
pmid = {39266944},
issn = {1471-2164},
support = {2023-PPI-007//Rockefeller Foundation/ ; },
mesh = {*High-Throughput Nucleotide Sequencing/methods ; *COVID-19/virology ; Humans ; *SARS-CoV-2/genetics ; *Metagenomics/methods ; Bacteria/genetics ; },
abstract = {BACKGROUND: The expansion of sequencing technologies as a result of the response to the COVID-19 pandemic enabled pathogen (meta)genomics to be deployed as a routine component of surveillance in many countries. Scaling genomic surveillance, however, comes with associated costs in both equipment and sequencing reagents, which should be optimized. Here, we evaluate the cost efficiency and performance of different read lengths in identifying pathogens in metagenomic samples. We carefully evaluated performance metrics, costs, and time requirements relative to choices of 75, 150 and 300 base pairs (bp) read lengths in pathogen identification.<br><br>RESULTS: Our findings revealed that moving from 75&#xa0;bp to 150&#xa0;bp read length approximately doubles both the cost and sequencing time. Opting for 300&#xa0;bp reads leads to approximately two- and three-fold increases, respectively, in cost and sequencing time compared to 75&#xa0;bp reads. For viral pathogen detection, the sensitivity median ranged from 99% with 75&#xa0;bp reads to 100% with 150-300&#xa0;bp reads. However, bacterial pathogens detection was less effective with shorter reads: 87% with 75&#xa0;bp, 95% with 150&#xa0;bp, and 97% with 300&#xa0;bp reads. These findings were consistent across different levels of taxa abundance. The precision of pathogen detection using shorter reads was comparable to that of longer reads across most viral and bacterial taxa.<br><br>CONCLUSIONS: During disease outbreak situations, when swift responses are required for pathogen identification, we suggest prioritizing 75&#xa0;bp read lengths, especially if detection of viral pathogens is aimed. This practical approach allows better use of resources, enabling the sequencing of more samples using streamlined workflows, while maintaining a reliable response capability.},
}
@article {pmid39266528,
year = {2024},
author = {Liu, S and Chen, Q and Hou, C and Dong, C and Qiu, X and Tang, K},
title = {Recovery of 1559 metagenome-assembled genomes from the East China Sea's low-oxygen region.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {994},
pmid = {39266528},
issn = {2052-4463},
mesh = {China ; *Metagenome ; *Archaea/genetics ; Bacteria/genetics/classification ; Oxygen ; Seawater/microbiology ; Phylogeny ; Metagenomics ; Oceans and Seas ; Microbiota ; },
abstract = {The Changjiang Estuary and adjacent East China Sea are well-known hypoxic aquatic environments. Eutrophication-driven hypoxia frequently occurs in coastal areas, posing a major threat to the ecological environment, including altering community structure and metabolic processes of marine organisms, and enhancing diversion of energy shunt into microbial communities. However, the responses of microbial communities and their metabolic pathways to coastal hypoxia remain poorly understood. Here, we studied the microbial communities collected from spatiotemporal samplings using metagenomic sequencing in the Changjiang Estuary and adjacent East China Sea. This generated 1.31 Tbp of metagenomics data, distributed across 103 samples corresponding to 8 vertical profiles. We further reported 1,559 metagenome-assembled genomes (MAGs), of which 508 were high-quality MAGs (Completeness > 90% and Contamination < 10%). Phylogenomic analysis classified them into 181 archaeal and 1,378 bacterial MAGs. These results provided a valuable metagenomic dataset available for further investigation of the effects of hypoxia on marine microorganisms.},
}
@article {pmid39266450,
year = {2024},
author = {Gnimpieba, EZ and Hartman, TW and Do, T and Zylla, J and Aryal, S and Haas, SJ and Agany, DDM and Gurung, BDS and Doe, V and Yosufzai, Z and Pan, D and Campbell, R and Huber, VC and Sani, R and Gadhamshetty, V and Lushbough, C},
title = {Biofilm marker discovery with cloud-based dockerized metagenomics analysis of microbial communities.},
journal = {Briefings in bioinformatics},
volume = {25},
number = {Supplement_1},
pages = {},
pmid = {39266450},
issn = {1477-4054},
support = {#1849206//National Science Foundation/ ; //Institutional Development Award/ ; /GM/NIGMS NIH HHS/United States ; P20GM103443/NH/NIH HHS/United States ; },
mesh = {*Biofilms/growth &amp; development ; *Metagenomics/methods ; Microbiota/genetics ; Cloud Computing ; Humans ; Computational Biology/methods ; },
abstract = {In an environment, microbes often work in communities to achieve most of their essential functions, including the production of essential nutrients. Microbial biofilms are communities of microbes that attach to a nonliving or living surface by embedding themselves into a self-secreted matrix of extracellular polymeric substances. These communities work together to enhance their colonization of surfaces, produce essential nutrients, and achieve their essential functions for growth and survival. They often consist of diverse microbes including bacteria, viruses, and fungi. Biofilms play a critical role in influencing plant phenotypes and human microbial infections. Understanding how these biofilms impact plant health, human health, and the environment is important for analyzing genotype-phenotype-driven rule-of-life functions. Such fundamental knowledge can be used to precisely control the growth of biofilms on a given surface. Metagenomics is a powerful tool for analyzing biofilm genomes through function-based gene and protein sequence identification (functional metagenomics) and sequence-based function identification (sequence metagenomics). Metagenomic sequencing enables a comprehensive sampling of all genes in all organisms present within a biofilm sample. However, the complexity of biofilm metagenomic study warrants the increasing need to follow the Findability, Accessibility, Interoperability, and Reusable (FAIR) Guiding Principles for scientific data management. This will ensure that scientific findings can be more easily validated by the research community. This study proposes a dockerized, self-learning bioinformatics workflow to increase the community adoption of metagenomics toolkits in a metagenomics and meta-transcriptomics investigation. Our biofilm metagenomics workflow self-learning module includes integrated learning resources with an interactive dockerized workflow. This module will allow learners to analyze resources that are beneficial for aggregating knowledge about biofilm marker genes, proteins, and metabolic pathways as they define the composition of specific microbial communities. Cloud and dockerized technology can allow novice learners-even those with minimal knowledge in computer science-to use complicated bioinformatics tools. Our cloud-based, dockerized workflow splits biofilm microbiome metagenomics analyses into four easy-to-follow submodules. A variety of tools are built into each submodule. As students navigate these submodules, they learn about each tool used to accomplish the task. The downstream analysis is conducted using processed data obtained from online resources or raw data processed via Nextflow pipelines. This analysis takes place within Vertex AI's Jupyter notebook instance with R and Python kernels. Subsequently, results are stored and visualized in Google Cloud storage buckets, alleviating the computational burden on local resources. The result is a comprehensive tutorial that guides bioinformaticians of any skill level through the entire workflow. It enables them to comprehend and implement the necessary processes involved in this integrated workflow from start to finish. This manuscript describes the development of a resource module that is part of a learning platform named "NIGMS Sandbox for Cloud-based Learning" https://github.com/NIGMS/NIGMS-Sandbox. The overall genesis of the Sandbox is described in the editorial NIGMS Sandbox [1] at the beginning of this Supplement. This module delivers learning materials on the analysis of bulk and single-cell ATAC-seq data in an interactive format that uses appropriate cloud resources for data access and analyses.},
}
@article {pmid39265854,
year = {2024},
author = {Viglioli, M and Rizzo, SM and Alessandri, G and Fontana, F and Milani, C and Turroni, F and Mancabelli, L and Croci, N and Rivara, S and Vacondio, F and Ventura, M and Mor, M},
title = {Investigating drug-gut microbiota interactions: reductive and hydrolytic metabolism of oral glucocorticoids by in vitro artificial gut microbiota.},
journal = {International journal of pharmaceutics},
volume = {665},
number = {},
pages = {124663},
doi = {10.1016/j.ijpharm.2024.124663},
pmid = {39265854},
issn = {1873-3476},
abstract = {Elucidation of the role of gut microbiota in the metabolism of orally administered drugs may improve therapeutic effectiveness and contribute to the development of personalized medicine. In this study, ten different artificial gut microbiota (AGM), obtained by culturing fecal samples in a continuous fermentation system, were challenged for their metabolizing capacity on a panel of six glucocorticoids selected from either prodrugs or drugs. Data from metabolic stability assays highlighted that, while the hydrolysis-mediated conversion of prodrugs to drugs represented only a minor metabolic pathway, significant differences in the stability of parent compounds and in their conversion rates to multiple reductive metabolites were obtained for the selected drugs. In the latter case, a taxonomic composition-dependent ability to convert parent drugs to metabolites was observed. Indeed, the artificial microbial communities dominated by the genus Bacteroides showed the maximal conversion of parent glucocorticoids to several metabolites. Furthermore, the effect of drugs on AGM was also evaluated through shallow shotgun sequencing and flow cytometry-based total bacterial cell count highlighting that these drugs can affect both the taxonomic composition and growth performances of the human gut microbiota.},
}
@article {pmid39265811,
year = {2024},
author = {Nataraj, BH and Ranveer, SA and K, J and Nagpal, R and Behare, PV},
title = {Immune and microbiome modulatory effects of Limosilactobacillus fermentum NCDC 400 in an immunocompromised mouse model.},
journal = {Microbial pathogenesis},
volume = {196},
number = {},
pages = {106927},
doi = {10.1016/j.micpath.2024.106927},
pmid = {39265811},
issn = {1096-1208},
abstract = {The present study was aimed to assess and validate the safety and functional efficacy of an indigenous probiotic strain Limosilactobacillus fermentum NCDC 400 (hereafter, LFN400) in an immunocompromised murine model. The study included four groups; a normal control (NC) group without immune suppression; an experimental model control (MC) with immune suppression induced via intraperitoneal cyclophosphamide (Cy) administration; and two MC groups orally administered with either low dose (LD) or high dose (HD) of LFN400 at dose 10[8] and 10[10] CFU/mouse/day, respectively, for 15-days. Both control groups received normal saline as placebo control. LFN400 improved specific experimental characteristics including hematological and serum biochemical markers. Compared to MC group, LFN400-fed groups showed markedly (P < 0.05) decreased arrays of detrimental caecal enzymes. We did not observe instances of bacterial translocation of LFN400 from gut to bloodstream or extra-intestinal organs. LFN400 intake significantly (P < 0.05) enhanced spleen cell differentiation, immune and oxidative stress markers, and restored Cy-induced histopathological changes in multiple tissues, including the spleen. There was no genotoxic effect of LFN400 on bone marrow cells. Although not statistically significant, LFN400 feeding moderately increased gut microbiome diversity, supporting the growth of beneficial saccharolytic microorganisms and reducing the presence of pathobionts. The findings demonstrate that the probiotic strain LFN400 possesses in vivo safety and immunomodulatory potency and thus should be considered a potential candidate for future human clinical studies.},
}
@article {pmid39265779,
year = {2024},
author = {Xiao, X and Wu, Y and Jie, Z and Lin, L and Li, Y and Hu, W and Li, Y and Zhong, S},
title = {Akkermansia Muciniphila supplementation improves hyperlipidemia, cardiac function, and gut microbiota in high fat fed apolipoprotein E-deficient mice.},
journal = {Prostaglandins &amp; other lipid mediators},
volume = {175},
number = {},
pages = {106906},
doi = {10.1016/j.prostaglandins.2024.106906},
pmid = {39265779},
issn = {1098-8823},
abstract = {Hyperlipidemia, obesity and gut dysbiosis are pivotal risk factors for atherosclerotic cardiovascular disease (ACVD). Supplementation of Akkermansia muciniphila (AKK) has also been proven to be effective in the prevention and treatment of obesity and other metabolic disorders. Here we found that AKK was more abundant in healthy control than ACVD patients via metagenomic sequencing on fecal samples. Subsequently, we investigated the role and underlying mechanism of AKK on obesity-associated atherosclerosis. AKK intervention partially reversed the exacerbation of atherosclerotic lesion formation in ApoE[-/-] mice by improving dyslipidemia. Interestingly, replenishment with AKK significantly enhanced cardiac function and reduced the body weight. It also reduced pro-inflammatory cytokine IL-6 and increased anti-inflammatory IL-10 in the circulation. Additionally, AKK colonization dramatically regulated gut microbiota and increased the abundance of Lactobacillaceae. Our findings have provided novel insights into the therapeutic potential of AKK as a beneficial microbe for treating atherosclerotic-associated cardiovascular diseases.},
}
@article {pmid39264803,
year = {2024},
author = {Tang, D and Hu, W and Fu, B and Zhao, X and You, G and Xie, C and Wang, HY and Guo, X and Zhang, Q and Liu, Z and Ye, L},
title = {Gut microbiota-mediated C-sulfonate metabolism impairs the bioavailability and anti-cholestatic efficacy of andrographolide.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2387402},
pmid = {39264803},
issn = {1949-0984},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Diterpenes/metabolism/pharmacology ; *Biological Availability ; Mice ; Cholestasis/metabolism/drug therapy/microbiology ; Male ; RNA, Ribosomal, 16S/genetics ; Bile Acids and Salts/metabolism ; Bacteria/metabolism/classification/genetics/drug effects/isolation &amp; purification ; Humans ; Mice, Inbred C57BL ; Liver/metabolism/drug effects ; Receptors, Cytoplasmic and Nuclear/metabolism/genetics ; Disease Models, Animal ; },
abstract = {Cholestatic liver injury results from the accumulation of toxic bile acids in the liver, presenting a therapeutic challenge with no effective treatment available to date. Andrographolide (AP) has exhibited potential as a treatment for cholestatic liver disease. However, its limited oral bioavailability poses a significant obstacle to harnessing its potent therapeutic properties and restricts its clinical utility. This limitation is potentially attributed to the involvement of gut microbiota in AP metabolism. In our study, employing pseudo-germ-free, germ-free and strain colonization animal models, along with 16S rRNA and shotgun metagenomic sequencing analysis, we elucidate the pivotal role played by gut microbiota in the C-sulfonate metabolism of AP, a process profoundly affecting its bioavailability and anti-cholestatic efficacy. Subsequent investigations pinpoint a specific enzyme, adenosine-5'-phosphosulfate (APS) reductase, predominantly produced by Desulfovibrio piger, which catalyzes the reduction of SO4[2-] to HSO3[-]. HSO3[-] subsequently interacts with AP, targeting its C=C unsaturated double bond, resulting in the formation of the C-sulfonate metabolite, 14-deoxy-12(R)-sulfo andrographolide (APM). Inhibition of APS reductase leads to a notable enhancement in AP bioavailability and anti-cholestatic efficacy. Furthermore, employing RNA sequencing analysis and farnesoid X receptor (FXR) knockout mice, our findings suggest that AP may exert its anti-cholestatic effects by activating the FXR pathway to promote bile acid efflux. In summary, our study unveils the significant involvement of gut microbiota in the C-sulfonate metabolism of AP and highlights the potential benefits of inhibiting APS reductase to enhance its therapeutic effects. These discoveries provide valuable insights into enhancing the clinical applicability of AP as a promising treatment for cholestatic liver injury.},
}
@article {pmid39264585,
year = {2024},
author = {Lou, H and Wang, X and Jiang, Q and Li, X and Yao, Y and Chen, Q and Chen, L and Zhang, S and Yu, Y and Liu, C and Zhou, H},
title = {Clinical evaluation of a highly multiplexed CRISPR-based diagnostic assay for diagnosing lower respiratory tract infection: a prospective cohort study.},
journal = {Infectious diseases (London, England)},
volume = {},
number = {},
pages = {1-11},
doi = {10.1080/23744235.2024.2402921},
pmid = {39264585},
issn = {2374-4243},
abstract = {OBJECTIVE: Accurate and rapid identification of causative pathogens is essential to guide the clinical management of lower respiratory tract infections (LRTIs). Here we conducted a single-centre prospective study in 284 patients suspected of lower respiratory tract infections to evaluate the utility of a nucleic acid test based on highly multiplexed polymerase chain reaction (PCR) and CRISPR-Cas12a.<br><br>METHODS: We determined the analytical and diagnostic performance of the CRISPR assay using a combination of reference standards, including conventional microbiological tests (CMTs), metagenomic Next-Generation Sequencing (mNGS), and clinical adjudication by a panel of experts on infectious diseases and microbiology.<br><br>RESULTS: The CRISPR assay showed a higher detection rate (63.0%) than conventional microbiological tests (38.4%) and was lower than metagenomic Next-Generation Sequencing (72.9%). In detecting polymicrobial infections, the positivity rate of the CRISPR assay (19.4%) was higher than conventional microbiological tests (3.5%) and lower than metagenomic Next-Generation Sequencing (28.9%). The overall diagnostic sensitivity of the CRISPR assay (67.8%) was higher than conventional microbiological tests (41.8%), and lower than metagenomic Next-Generation Sequencing (93.2%).<br><br>CONCLUSIONS: Considering the low cost, ease of operation, short turnaround time, and broad range of pathogens detected in a single test, the CRISPR assay has the potential to be implemented as a screening tool for the aetiological diagnosis of lower respiratory tract infections patients, especially in cases where atypical bacteria or coinfections are suspected.},
}
@article {pmid39264513,
year = {2024},
author = {Angebault, C and Botterel, F},
title = {Metagenomics Applied to the Respiratory Mycobiome in Cystic Fibrosis.},
journal = {Mycopathologia},
volume = {189},
number = {5},
pages = {82},
pmid = {39264513},
issn = {1573-0832},
mesh = {*Cystic Fibrosis/microbiology/complications ; Humans ; *Mycobiome ; *Metagenomics/methods ; Fungi/genetics/classification/isolation &amp; purification ; Respiratory System/microbiology ; Bacteria/genetics/classification/isolation &amp; purification ; Lung/microbiology ; Microbiota ; },
abstract = {Cystic fibrosis (CF) is a genetic disorder characterized by chronic microbial colonization and inflammation of the respiratory tract (RT), leading to pulmonary exacerbation (PEx) and lung damage. Although the lung bacterial microbiota has been extensively studied, the mycobiome remains understudied. However, its importance as a contributor to CF pathophysiology has been highlighted. The objective of this review is to provide an overview of the current state of knowledge regarding the mycobiome, as described through NGS-based studies, in patients with CF (pwCF).Several studies have demonstrated that the mycobiome in CF lungs is a dynamic entity, exhibiting a lower diversity and abundance than the bacterial microbiome. Nevertheless, the progression of lung damage is associated with a decrease in fungal and bacterial diversity. The core mycobiome of the RT in pwCFs is mainly composed of yeasts (Candida spp., Malassezia spp.) and molds with lower abundance. Some fungi (Aspergillus, Scedosporium/Pseudallescheria) have been demonstrated to play a role in PEx, while the involvement of others (Candida, Pneumocystis) remains uncertain. The "climax attack" ecological model has been proposed to explain the complexity and interplay of microbial populations in the RT, leading to PEx and lung damage. NGS-based studies also enable the detection of intra- and interkingdom correlations between fungi and bacteria. Further studies are required to ascertain the biological and pathophysiological relevance of these correlations. Finally, with the recent advent of CFTR modulators, our understanding of the pulmonary microbiome and mycobiome in pwCFs is about to change.},
}
@article {pmid39264158,
year = {2024},
author = {Wang, X and Guo, X and Liu, H and Wang, B and Wu, J and Chen, S and Zhang, W and Zhang, X and Wang, X},
title = {Augmented pathogen detection in brain abscess using metagenomic next-generation sequencing: a retrospective cohort study.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0032524},
doi = {10.1128/spectrum.00325-24},
pmid = {39264158},
issn = {2165-0497},
abstract = {Brain abscess is a severe infection characterized by the accumulation of pus within the brain parenchyma. Accurate identification of the causative pathogens is crucial for effective treatment and improved patient outcomes. This 10-year retrospective, single-center study aimed to compare the detection performance of conventional culture methods and metagenomic next-generation sequencing (mNGS) in brain abscess. We reviewed 612 patients diagnosed with brain abscess and identified 174 cases with confirmed etiology. The median age was 52 years, with 69.5% males. Culture tests predominately identified gram-positive bacteria, particularly Streptococcus spp. Gram-negative bacteria, including Klebsiella spp., were also detected. However, mNGS revealed a more diverse pathogen spectrum, focusing on anaerobes (e.g., Fusobacterium spp., Parvimonas spp., Porphyromonas spp., Prevotella spp., and Tannerella spp.). mNGS exhibited significantly higher overall pathogen-positive rates in pus samples (85.0% vs 50.0%, P = 0.0181) and CSF samples (84.2% vs 7.9%, P < 0.0001) compared to culture. Furthermore, the detection rates for anaerobes displayed a notable disparity, with mNGS yielding significantly higher positive detections in both pus samples (50.0% vs 10%, P = 0.0058) and CSF samples (18.4% vs 0%, P = 0.0115) when compared to culture methods. The assistance of mNGS in pathogen detection, particularly anaerobes in brain abscess, was evident in our findings. mNGS demonstrated the ability to identify rare and fastidious pathogens, even in culture-negative cases. These results emphasize the clinical value of mNGS as a supplement for brain abscess, enabling more comprehensive and accurate pathogen identification.IMPORTANCEThe accurate identification of pathogens causing brain abscess is crucial for effective treatment and improved patient outcomes. In this 10-year retrospective study, the detection performance of conventional culture methods and metagenomic next-generation sequencing (mNGS) was compared. The study analyzed 612 patients with brain abscess and confirmed etiology in 174 cases. The results showed that culture tests predominantly identified gram-positive bacteria, while mNGS unveiled a broader diverse pathogen spectrum, particularly anaerobes. The mNGS method exhibited significantly higher overall rates of pathogen positivity both in pus and cerebrospinal fluid (CSF) samples, surpassing the culture methods. Notably, mNGS detected a significantly higher number of anaerobes in both pus and CSF samples compared to culture methods. These findings underscore the clinical value of mNGS as a supplement for brain abscess diagnosis, enabling more comprehensive and accurate pathogen identification, particularly for rare and fastidious pathogens that evade detection by conventional culture methods.},
}
@article {pmid39264053,
year = {2024},
author = {Ho, L and Lai, C and Daim, LDJ and Noh, NM and Yap, Y and Ibrahim, J and Teh, C},
title = {Deciphering Root-associated Microbial Communities in Asymptomatic Oil Palm Seedlings Exposed to Ganoderma boninense: New Insight into Disease Tolerance of Oil Palms.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiae122},
pmid = {39264053},
issn = {1574-6941},
abstract = {Understanding the microbial communities in asymptomatic oil palm seedlings is crucial for developing disease-suppressive microbiota against basal stem rot (BSR) in oil palm. In this study, we compared the microbial communities in bulk soil, rhizosphere, and endosphere of control, asymptomatic, and symptomatic seedlings following inoculation with Ganoderma boninense. Our findings revealed significant shifts in microbial structure and interactions, particularly in asymptomatic seedlings. Both Actinobacteriota and Ascomycota were notably enriched in these samples, with Actinobacteriota identified as keystone taxa. Long-read shotgun metagenomics demonstrated that 67.4% of enriched Actinobacteriota taxa were unique to asymptomatic seedlings. Similarly, Ascomycota members showed significant enrichment, suggesting their potential role in BSR suppression. The consistent identification of these phyla across various analyses underscores their importance in disease resistance. This is the first report detailing the shifts in prokaryotic and fungal communities in asymptomatic and symptomatic seedlings, offering insights into potential disease-suppressive taxa across three compartments: bulk soil, rhizosphere, and endosphere of oil palm seedlings.},
}
@article {pmid39263696,
year = {2024},
author = {Nag, M and Pallavi, J and Chakraborty, S and Roychoudhury, T and Mondal, S and Ghosh, A and Saha, C and Banerjee, M and Seal, A},
title = {Bacterial endosymbionts of a nitrogen-fixing yeast Rhodotorula mucilaginosa JGTA-S1 - insights into a yet unknown micro-ecosystem.},
journal = {Molecular omics},
volume = {},
number = {},
pages = {},
doi = {10.1039/d3mo00273j},
pmid = {39263696},
issn = {2515-4184},
abstract = {Rhodotorula mucilaginosa JGTA-S1 is a yeast strain capable of fixing nitrogen and improving nitrogen nutrition in rice plants because of its nitrogen-fixing endobacteria, namely Stutzerimonas (Pseudomonas) stutzeri and Bradyrhizobium sp. To gain a deeper understanding of yeast endosymbionts, we conducted a whole-genome shotgun metagenomic analysis of JGTA-S1 cells grown under conditions of nitrogen sufficiency and deficiency. Our results showed that the endosymbiont population varied depending on the nitrogen regime. Upon mechanical disruption of yeast cells, we obtained endosymbionts in culturable form viz. Bacillus velezensis and Staphylococcus sp. under nitrogen-replete conditions and Lysinibacillus telephonicus., Brevibacillus sp., and Niallia circulans under nitrogen-depleted conditions. S. stutzeri and Bradyrhizobium sp. the previously reported endosymbionts remained unculturable. The culturable endosymbionts Staphylococcus sp. and Bacillus velezensis appear to possess genes for dissimilatory nitrate reduction (DNRA), an alternative pathway for ammonia synthesis. However, our findings suggest that these endosymbionts are facultative as they survive outside the host. The fitness of the yeast was not affected by curing of these microbes. Curing the yeast diazotrophic endosymbionts took a toll on its fitness. Our results also showed that the populations of S. stutzeri and B. velezensis increased significantly under nitrogen-depleted conditions compared to nitrogen-sufficient conditions. The importance of DNRA and nitrogen fixation is also reflected in the metagenomic reads of JGTA-S1.},
}
@article {pmid39263550,
year = {2024},
author = {Bell, E and Chen, J and Richardson, WDL and Fustic, M and Hubert, CRJ},
title = {Denitrification genotypes of endospore-forming Bacillota.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae107},
pmid = {39263550},
issn = {2730-6151},
abstract = {Denitrification is a key metabolic process in the global nitrogen cycle and is performed by taxonomically diverse microorganisms. Despite the widespread importance of this metabolism, challenges remain in identifying denitrifying populations and predicting their metabolic end-products based on their genotype. Here, genome-resolved metagenomics was used to explore the denitrification genotype of Bacillota enriched in nitrate-amended high temperature incubations with confirmed N2O and N2 production. A set of 12 hidden Markov models (HMMs) was created to target the diversity of denitrification genes in members of the phylum Bacillota. Genomic potential for complete denitrification was found in five metagenome-assembled genomes from nitrate-amended enrichments, including two novel members of the Brevibacillaceae family. Genomes of complete denitrifiers encode N2O reductase gene clusters with clade II-type nosZ and often include multiple variants of the nitric oxide reductase gene. The HMM set applied to all genomes of Bacillota from the Genome Taxonomy Database identified 17 genera inferred to contain complete denitrifiers based on their gene content. Among complete denitrifiers it was common for three distinct nitric oxide reductases to be present (qNOR, bNOR, and sNOR) that may reflect the metabolic adaptability of Bacillota in environments with variable redox conditions.},
}
@article {pmid39263297,
year = {2024},
author = {Wang, A and Cui, X and Shi, C},
title = {Metagenomic analysis of rats with diarrhea treated with mixed probiotics: response to consecutive and alternate-hour supplementation.},
journal = {Translational pediatrics},
volume = {13},
number = {8},
pages = {1336-1358},
pmid = {39263297},
issn = {2224-4344},
abstract = {BACKGROUND: Diarrhea is the leading contributory factor of sickness and mortality among children under five and an economic burden for families. This study aimed to investigate the effects of mixed probiotics supplementation at different times (consecutive and alternate-hour) on intestinal microecology in Sprague-Dawley (SD) rats with acute diarrhea.<br><br>METHODS: A total of 40 SD rats were randomly assigned to four groups, including the control group, model group, probiotic group A, and probiotic group B. An acute diarrhea model was induced by administration of 5% dextran sulfate sodium. Rats in probiotic group A and probiotic group B were fed with Clostridium butyricum (C. butyricum), Bifidobacterium infantis (B. infantis), and Saccharomyces boulardii (S. boulardii) for a total of 7 days. Probiotic group A was fed with all probiotics simultaneously. Probiotic group B was fed with C. butyricum and B. infantis simultaneously, and then after a 2-hour interval, with S. boulardii. Metagenomic next-generation sequencing was used to analyze the fecal samples from every rat. The metagenomic sequencing used in this experiment was used to evaluate the effect of probiotics on the composition as well as function of the gut microbiota in order to gain a deeper comprehension of probiotic-host interactions on health and disease.<br><br>RESULTS: The structure of the gut microbiota in probiotic group A showed significant changes. Compared to the model group, the abundance of some beneficial bacteria had increased, including Actinobacteria (P=0.048), Lactobacillus (P=0.050), and Lactobacillus johnsonii (P=0.042), and many opportunistic pathogenic bacteria has decreased, such as Ruminococcus (P=0.001). Compared to the control group, the abundance of some beneficial bacteria had increased, including Fusobacteria (P=0.02) and Phascolarium (P=0.002), and there was a reduction in the abundance of many opportunistic pathogenic bacteria such as Roseburia (P=0.03), Lachnoclosterium (P=0.009), and Oscillibacter_sp_1-3 (P=0.002). In addition, metagenomic analysis showed that as well as an up-regulation of glycoside hydrolase expression, amino acid and inorganic ion transport, and metabolism-related pathways, there was a down-regulation of cell motility.<br><br>CONCLUSIONS: Simultaneous administration of probiotics may have more positive implications in improving the gut microbiota of acute diarrhea rats.},
}
@article {pmid39262445,
year = {2023},
author = {Borry, M and Forsythe, A and Andrades Valtueña, A and Hübner, A and Ibrahim, A and Quagliariello, A and White, AE and Kocher, A and Vågene, &#xc5;J and Bartholdy, BP and Spurīte, D and Ponce-Soto, GY and Neumann, G and Huang, IT and Light, I and Velsko, IM and Jackson, I and Frangenberg, J and Serrano, JG and Fumey, J and Özdoğan, KT and Blevins, KE and Daly, KG and Lopopolo, M and Moraitou, M and Michel, M and van Os, M and Bravo-Lopez, MJ and Sarhan, MS and Dagtas, ND and Oskolkov, N and Smith, OS and Lebrasseur, O and Rozwalak, P and Eisenhofer, R and Wasef, S and Ramachandran, SL and Vanghi, V and Warinner, C and Fellows Yates, JA},
title = {Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT.},
journal = {F1000Research},
volume = {12},
number = {},
pages = {926},
pmid = {39262445},
issn = {2046-1402},
mesh = {*Metagenomics/methods ; Humans ; *Metadata ; High-Throughput Nucleotide Sequencing/methods ; Software ; Metagenome ; Computational Biology/methods ; DNA, Ancient/analysis ; },
abstract = {BACKGROUND: Access to sample-level metadata is important when selecting public metagenomic sequencing datasets for reuse in new biological analyses. The Standards, Precautions, and Advances in Ancient Metagenomics community (SPAAM, https://spaam-community.org) has previously published AncientMetagenomeDir, a collection of curated and standardised sample metadata tables for metagenomic and microbial genome datasets generated from ancient samples. However, while sample-level information is useful for identifying relevant samples for inclusion in new projects, Next Generation Sequencing (NGS) library construction and sequencing metadata are also essential for appropriately reprocessing ancient metagenomic data. Currently, recovering information for downloading and preparing such data is difficult when laboratory and bioinformatic metadata is heterogeneously recorded in prose-based publications.<br><br>METHODS: Through a series of community-based hackathon events, AncientMetagenomeDir was updated to provide standardised library-level metadata of existing and new ancient metagenomic samples. In tandem, the companion tool 'AMDirT' was developed to facilitate rapid data filtering and downloading of ancient metagenomic data, as well as improving automated metadata curation and validation for AncientMetagenomeDir.<br><br>RESULTS: AncientMetagenomeDir was extended to include standardised metadata of over 6000 ancient metagenomic libraries. The companion tool 'AMDirT' provides both graphical- and command-line interface based access to such metadata for users from a wide range of computational backgrounds. We also report on errors with metadata reporting that appear to commonly occur during data upload and provide suggestions on how to improve the quality of data sharing by the community.<br><br>CONCLUSIONS: Together, both standardised metadata reporting and tooling will help towards easier incorporation and reuse of public ancient metagenomic datasets into future analyses.},
}
@article {pmid39262440,
year = {2024},
author = {Hallgren, MB and Clausen, PTLC and Aarestrup, FM},
title = {NanoMGT: Marker gene typing of low complexity mono-species metagenomic samples using noisy long reads.},
journal = {Biology methods &amp; protocols},
volume = {9},
number = {1},
pages = {bpae057},
pmid = {39262440},
issn = {2396-8923},
abstract = {Rapid advancements in sequencing technologies have led to significant progress in microbial genomics, yet challenges persist in accurately identifying microbial strain diversity in metagenomic samples, especially when working with noisy long-read data from platforms like Oxford Nanopore Technologies (ONT). In this article, we introduce NanoMGT, a tool designed to enhance marker gene typing in low-complexity mono-species samples, leveraging the unique properties of long reads. NanoMGT excels in its ability to accurately identify mutations amidst high error rates, ensuring the reliable detection of multiple strain-specific marker genes. Our tool implements a novel scoring system that rewards mutations co-occurring across different reads and penalizes densely grouped, likely erroneous variants, thereby achieving a good balance between sensitivity and precision. A comparative evaluation of NanoMGT, using a simulated multi-strain sample of seven bacterial species, demonstrated superior performance relative to existing tools and the advantages of using a threshold-based filtering approach to calling minority variants in ONT's sequencing data. NanoMGT's potential as a post-binning tool in metagenomic pipelines is particularly notable, enabling researchers to more accurately determine specific alleles and understand strain diversity in microbial communities. Our findings have significant implications for clinical diagnostics, environmental microbiology, and the broader field of genomics. The findings offer a reliable and efficient approach to marker gene typing in complex metagenomic samples.},
}
@article {pmid39261970,
year = {2024},
author = {Wan, X and Shahrear, S and Chew, SW and Vilaplana, F and Mäkelä, MR},
title = {Discovery of alkaline laccases from basidiomycete fungi through machine learning-based approach.},
journal = {Biotechnology for biofuels and bioproducts},
volume = {17},
number = {1},
pages = {120},
pmid = {39261970},
issn = {2731-3654},
support = {NNF21OC0071410//Novo Nordisk Fonden/ ; HiLIFE Fellows grant 2023-2025//Helsinki Institute of Life Science, Helsingin Yliopisto/ ; },
abstract = {BACKGROUND: Laccases can oxidize a broad spectrum of substrates, offering promising applications in various sectors, such as bioremediation, biomass fractionation in future biorefineries, and synthesis of biochemicals and biopolymers. However, laccase discovery and optimization with a desirable pH optimum remains a challenge due to the labor-intensive and time-consuming nature of the traditional laboratory methods.<br><br>RESULTS: This study presents a machine learning (ML)-integrated approach for predicting pH optima of basidiomycete fungal laccases, utilizing a small, curated dataset against a vast metagenomic data. Comparative computational analyses unveiled the structural and pH-dependent solubility differences between acidic and neutral-alkaline laccases, helping us understand the molecular bases of enzyme pH optimum. The pH profiling of the two ML-predicted alkaline laccase candidates from the basidiomycete fungus Lepista nuda further validated our computational approach, showing the accuracy of this comprehensive method.<br><br>CONCLUSIONS: This study uncovers the efficacy of ML in the prediction of enzyme pH optimum from minimal datasets, marking a significant step towards harnessing computational tools for systematic screening of enzymes for biotechnology applications.},
}
@article {pmid39261503,
year = {2024},
author = {Schwab, S and Hu, Y and van Erp, B and Cajili, MKM and Hartmann, MD and Hernandez Alvarez, B and Alva, V and Boyle, AL and Dame, RT},
title = {Histones and histone variant families in prokaryotes.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {7950},
pmid = {39261503},
issn = {2041-1723},
support = {OCENW.GROOT.2019.012//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; },
mesh = {*Histones/metabolism/chemistry/genetics ; *Archaea/metabolism/genetics ; *Bacteria/metabolism/genetics ; Prokaryotic Cells/metabolism ; Phylogeny ; Nucleosomes/metabolism ; Models, Molecular ; Archaeal Proteins/metabolism/chemistry/genetics ; Amino Acid Sequence ; },
abstract = {Histones are important chromatin-organizing proteins in eukaryotes and archaea. They form superhelical structures around which DNA is wrapped. Recent studies have shown that some archaea and bacteria contain alternative histones that exhibit different DNA binding properties, in addition to highly divergent sequences. However, the vast majority of these histones are identified in metagenomes and thus are difficult to study in vivo. The recent revolutionary breakthroughs in computational protein structure prediction by AlphaFold2 and RoseTTAfold allow for unprecedented insights into the potential function and structure of previously uncharacterized proteins. Here, we categorize the prokaryotic histone space into 17 distinct groups based on AlphaFold2 predictions. We identify a superfamily of histones, termed α3 histones, which are common in archaea and present in several bacteria. Importantly, we establish the existence of a large family of histones throughout archaea and in some bacteriophages that, instead of wrapping DNA, bridge DNA, thereby diverging from conventional nucleosomal histones.},
}
@article {pmid39260724,
year = {2024},
author = {Ke, Y and Sun, W and Xue, Y and Yuan, Z and Zhu, Y and Chen, X and Yan, S and Li, Y and Xie, S},
title = {Pipe material and natural organic matter impact drinking water biofilm microbial community, pathogen profiles and antibiotic resistome deciphered by metagenomics assembly.},
journal = {Environmental research},
volume = {262},
number = {Pt 2},
pages = {119964},
doi = {10.1016/j.envres.2024.119964},
pmid = {39260724},
issn = {1096-0953},
abstract = {Biofilms in drinking water distribution systems (DWDSs) are a determinant to drinking water biosafety. Yet, how and why pipe material and natural organic matter (NOM) affect biofilm microbial community, pathogen composition and antibiotic resistome remain unclear. We characterized the biofilms' activity, microbial community, antibiotic resistance genes (ARGs), mobile genetic elements (MGEs) and pathogenic ARG hosts in Centers for Disease Control and Prevention (CDC) reactors with different NOM dosages and pipe materials based on metagenomics assembly. Biofilms in cast iron (CI) pipes exhibited higher activity than those in polyethylene (PE) pipes. NOM addition significantly decreased biofilm activity in CI pipes but increased it in PE pipes. Pipe material exerted more profound effects on microbial community structure than NOM. Azospira was significantly enriched in CI pipes and Sphingopyxis was selected in PE pipes, while pathogen (Ralstonia pickettii) increased considerably in NOM-added reactors. Microbial community network in CI pipes showed more edges (CI 13520, PE 7841) and positive correlation proportions (CI 72.35%, PE 61.69%) than those in PE pipes. Stochastic processes drove assembly of both microbial community and antibiotic resistome in DWDS biofilms based on neutral community model. Bacitracin, fosmidomycin and multidrug ARGs were predominant in both PE and CI pipes. Both pipe materials and NOM regulated the biofilm antibiotic resistome. Plasmid was the major MGE co-existing with ARGs, facilitating ARG horizontal transfer. Pathogens (Achromobacter xylosoxidans and Ralstonia pickettii) carried multiple ARGs (qacEdelta1, OXA-22 and aadA) and MGEs (integrase, plasmid and transposase), which deserved more attention. Microbial community contributed more to ARG change than MGEs. Structure equation model (SEM) demonstrated that turbidity and ammonia affected ARGs by directly mediating Shannon diversity and MGEs. These findings might provide a technical guidance for controlling pathogens and ARGs from the point of pipe material and NOM in drinking water.},
}
@article {pmid39260513,
year = {2024},
author = {Tan, J and Wang, Y and Niu, H and Li, L and Zhao, H and Fang, L and Jiang, L and Zhao, Y},
title = {Metagenomic insights into the mechanistic differences of plant polyphenols and nitrocompounds in reducing methane emissions using the rumen simulation technique.},
journal = {The Science of the total environment},
volume = {953},
number = {},
pages = {176135},
doi = {10.1016/j.scitotenv.2024.176135},
pmid = {39260513},
issn = {1879-1026},
abstract = {Methane (CH4) emissions from ruminants contribute significantly to greenhouse gas levels and also result in considerable feed energy losses. Plant polyphenols and nitrocompounds are two typical types of methane inhibitors. The study investigates the mechanistic differences between 2-nitroethanol (NE) and proanthocyanidins (PAC) in reducing methane emissions from ruminant livestock using the rumen simulation technique (RUSITEC) combined with metagenomic analyses. The experiment was performed as a complete randomized block design with 3 runs. Run was used as a blocking factor. The treatments included a control (CON) with no additive, NE at 0.5 g/kg dry matter (DM), and PAC at 20 g/kg DM, all incubated in vitro for 24 h (h) with eight replicates per treatment. The results showed that NE significantly reduced CH4 production by 94.9 % (P < 0.01) and total volatile fatty acid (TVFA) concentration by 11.1 % (P < 0.05) compared to the control. NE also decreased the acetate-to-propionate ratio (A/P) from 1.93 to 1.60 (P < 0.01), indicating a shift towards more efficient fermentation. In contrast, PAC reduced methane production by 11.7 % (P < 0.05) and decreased the A/P (P < 0.05) while maintaining microbial diversity and fermentation stability, with no significant impact on TVFA concentration (P > 0.05). Metagenomic analysis revealed that NE markedly suppressed the abundance of key genera involved in carbohydrate metabolism, including Prevotella and Bacteroides, leading to reduced acetate and butyrate pathways. NE also selectively inhibited methanogenic archaea, particularly Methanobrevibacter spp., which are integral to the hydrogenotrophic pathway (P < 0.01). On the other hand, PAC showed selective inhibition of Methanosphaera spp., targeting the methylotrophic pathway (P < 0.01). These findings provide valuable insights into the distinct microbial and metabolic pathways modulated by NE and PAC, offering potential strategies for developing effective dietary interventions to mitigate methane emissions in ruminant livestock.},
}
@article {pmid39260494,
year = {2024},
author = {Ejaz, MR and Badr, K and Hassan, ZU and Al-Thani, R and Jaoua, S},
title = {Metagenomic approaches and opportunities in arid soil research.},
journal = {The Science of the total environment},
volume = {953},
number = {},
pages = {176173},
doi = {10.1016/j.scitotenv.2024.176173},
pmid = {39260494},
issn = {1879-1026},
abstract = {Arid soils present unique challenges and opportunities for studying microbial diversity and bioactive potential due to the extreme environmental conditions they bear. This review article investigates soil metagenomics as an emerging tool to explore complex microbial dynamics and unexplored bioactive potential in harsh environments. Utilizing advanced metagenomic techniques, diverse microbial populations that grow under extreme conditions such as high temperatures, salinity, high pH levels, and exposure to metals and radiation can be studied. The use of extremophiles to discover novel natural products and biocatalysts emphasizes the role of functional metagenomics in identifying enzymes and secondary metabolites for industrial and pharmaceutical purposes. Metagenomic sequencing uncovers a complex network of microbial diversity, offering significant potential for discovering new bioactive compounds. Functional metagenomics, connecting taxonomic diversity to genetic capabilities, provides a pathway to identify microbes' mechanisms to synthesize valuable secondary metabolites and other bioactive substances. Contrary to the common perception of desert soil as barren land, the metagenomic analysis reveals a rich diversity of life forms adept at extreme survival. It provides valuable findings into their resilience and potential applications in biotechnology. Moreover, the challenges associated with metagenomics in arid soils, such as low microbial biomass, high DNA degradation rates, and DNA extraction inhibitors and strategies to overcome these issues, outline the latest advancements in extraction methods, high-throughput sequencing, and bioinformatics. The importance of metagenomics for investigating diverse environments opens the way for future research to develop sustainable solutions in agriculture, industry, and medicine. Extensive studies are necessary to utilize the full potential of these powerful microbial communities. This research will significantly improve our understanding of microbial ecology and biotechnology in arid environments.},
}
@article {pmid39260483,
year = {2024},
author = {Li, W and Wang, H and Lv, G and Wang, J and Li, J},
title = {Regulation of drought stress on nutrient cycle and metabolism of rhizosphere microorganisms in desert riparian forest.},
journal = {The Science of the total environment},
volume = {954},
number = {},
pages = {176148},
doi = {10.1016/j.scitotenv.2024.176148},
pmid = {39260483},
issn = {1879-1026},
abstract = {Microbial communities in desert riparian forest ecosystems have developed unique adaptive strategies to thrive in harsh habitats shaped by prolonged exposure to abiotic stressors. However, the influence of drought stress on the functional and metabolic characteristics of soil rhizosphere microorganisms remains unknown. Therefore, this study aimed to investigate the effects of drought stress on soil biogeochemistry and metabolism and analyze the relationship between the biogeochemical cycle processes and network of differentially-expressed metabolites. Using metagenomics and metabolomics, this study explored the microbial functional cycle and differential metabolic pathways within desert riparian forests. The predominant biogeochemical cycles in the study area were the Carbon and Nitrogen cycles, comprising 78.90 % of C, N, Phosphorus, Sulfur and Iron cycles. Drought led to increased soil C fixation, reduced C degradation and methane metabolism, weakened denitrification, and decreased N fixation. Furthermore, drought can disrupt iron homeostasis and reduce its absorption. The differential metabolic pathways of drought stress include flavonoid biosynthesis, arachidonic acid metabolism, steroid hormone biosynthesis, and starch and sucrose degradation. Network analysis of functional genes and metabolism revealed a pronounced competitive relationship between the C cycle and metabolic network, whereas the Fe cycle and metabolic network promoted each other, optimizing resource utilization. Partial least squares analysis revealed that drought hindered the expression and metabolic processes and functional genes, whereas the rhizosphere environment facilitated metabolic expression and the functional genes. The rhizosphere effect primarily promoted metabolic processes indirectly through soil enzyme activities. The integrated multi-omics analysis further revealed that the effects of drought and the rhizosphere play a predominant role in shaping soil functional potential and the accumulation of metabolites. These insights deepen our comprehension of desert riparian forest ecosystems and offer strong support for the functionality of nutrient cycling and metabolite dynamics.},
}
@article {pmid39260018,
year = {2024},
author = {Chen, M and Chen, Y and He, X and Hao, R and Jiang, X and Ji, Y and Zhuo, B and Xu, W and Lin, R and Ge, Y},
title = {A case of Bartonella vinsonii endocarditis.},
journal = {Diagnostic microbiology and infectious disease},
volume = {110},
number = {4},
pages = {116535},
doi = {10.1016/j.diagmicrobio.2024.116535},
pmid = {39260018},
issn = {1879-0070},
abstract = {The diagnosis of Bartonella is challenging due to its rarity and negative culture results. Once the diagnosis is delayed and proper treatment is not given, it can develop into infective endocarditis, which can be fatal. We reported a 60-year-old female patient who had recurrent fever for 5 months. After receiving ineffective treatment at the local hospital, she sought medical attention at our hospital. Laboratory blood indicators testing and imaging indicated infective endocarditis, and metagenomic Next Generation Sequencing (m-NGS) testing confirmed the diagnosis of Bartonella vinsonii infection. After surgical treatment and the combination of doxycycline and ceftriaxone sodium for anti-infective therapy, the patient recovered. Valuing the combination of multiple auxiliary diagnostic methods and improving the application of m-NGS in the detection of unknown pathogens can compensate for the current limitations in the diagnosis of Bartonella. Early diagnosis and treatment are extremely important for Bartonella endocarditis.},
}
@article {pmid39259188,
year = {2024},
author = {Liu, C and Wang, Y and Zhou, Z and Wang, S and Wei, Z and Ravanbakhsh, M and Shen, Q and Xiong, W and Kowalchuk, GA and Jousset, A},
title = {Protist predation promotes antimicrobial resistance spread through antagonistic microbiome interactions.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae169},
pmid = {39259188},
issn = {1751-7370},
abstract = {None declared.Conflicts of interestAntibiotic resistance has grown into a major public health threat. In this study, we reveal predation by protists as an overlooked driver of antibiotic resistance dissemination in the soil microbiome. While previous studies have primarily focused on the distribution of antibiotic resistance genes, our work sheds light on the pivotal role of soil protists in shaping antibiotic resistance dynamics. Using a combination of metagenomics and controlled experiments in this study, we demonstrate that protists cause an increase in antibiotic resistance. We mechanistically link this increase to a fostering of antimicrobial activity in the microbiome. Protist predation gives a competitive edge to bacteria capable of producing antagonistic secondary metabolites, which secondary metabolites promote in turn antibiotic-resistant bacteria. This study provides insights into the complex interplay between protists and soil microbiomes in regulating antibiotic resistance dynamics. This study highlights the importance of top-down control on the spread of antibiotic resistance and directly connects it to cross-kingdom interactions within the microbiome. Managing protist communities may become an important tool to control outbreaks of antibiotic resistance in the environment.},
}
@article {pmid39258944,
year = {2024},
author = {Zhu, W and Zeng, Z and Xia, J and Li, L},
title = {Achieving rapid start-up and efficient nitrogen removal of partial-denitrification/anammox process using organic matter in brewery wastewater as carbon source.},
journal = {Environmental technology},
volume = {},
number = {},
pages = {1-13},
doi = {10.1080/09593330.2024.2401157},
pmid = {39258944},
issn = {1479-487X},
abstract = {To find a cost-efficient carbon source for the partial denitrification/anaerobic ammonium oxidation (anammox) (PD/A) process, the practicability of using the organic matter contained in brewery wastewater as carbon source was investigated. Quick self-enrichment of denitrifying bacteria was achieved by supplying brewery wastewater as organic carbon source and using the mature anammox sludge as the seeding sludge. The PD/A process was successfully established after 33-day operation and then the average total nitrogen removal efficiency reached 92.29% when the influent CODCr: NO3[-]-N: NH4[+]-N ratio was around 2.5: 1.0: 0.67. The relative abundance of Thauera increased from 0.03% in the seeding sludge to 54.29% on day 110, whereas Candidatus brocadia decreased from 30.66% to 2.08%. The metagenomic analysis indicated that the sludge on day 110 contained more nar and napA (total of 41.24%) than nirK and nirS (total of 11.93%). Thus NO2[-]-N was accumulated efficiently in the process of denitrification and sufficient NO2[-]-N was supplied for anammox bacteria in the PD/A process. Using brewery wastewater as carbon source not only saved the cost of nitrogen removal but also converted waste into resource and reduced the treatment expense of brewery wastewater.},
}
@article {pmid39258715,
year = {2024},
author = {Vats, R and Yadav, P and Bano, A and Wadhwa, S and Bhardwaj, R},
title = {Salivary biomarkers in non-invasive oral cancer diagnostics: a comprehensive review.},
journal = {Journal of applied oral science : revista FOB},
volume = {32},
number = {},
pages = {e20240151},
doi = {10.1590/1678-7757-2024-0151},
pmid = {39258715},
issn = {1678-7765},
mesh = {Humans ; *Mouth Neoplasms/diagnosis ; *Saliva/chemistry/virology ; *Biomarkers, Tumor/analysis ; Early Detection of Cancer/methods ; },
abstract = {OBJECTIVE: This review aims to provide a comprehensive analysis of the effectiveness of saliva as a non-invasive diagnostic marker for oral cancer. Despite progress in oral cancer diagnosis and prognosis, the 5-year survival rate remains low due to the resistance to treatment and delayed diagnosis, which can be attributed to various factors including tobacco and alcohol consumption, genetic damage, and human papillomavirus (HPV). The potential use of saliva as an easily accessible non-invasive screening and diagnostic method arises from its direct contact with the lesion site.<br><br>METHODOLOGY: Data for this study were gathered via a comprehensive literature evaluation using search engines such as the PubMed, Web of Science, Google Scholar, and SciFinder.<br><br>RESULTS: Identifying salivary biomarkers shows potential to transform oral cancer diagnostics by offering a reliable alternative to the traditional invasive methods. Saliva is an abundant reservoir for both cell-bound and cell-free organic and inorganic constituents. Thus, saliva is an appropriate field for research in proteomics, genomics, metagenomics, and metabolomics.<br><br>CONCLUSION: This review provides a comprehensive elucidation of salivary biomarkers and their function in non-invasive oral cancer diagnosis, demonstrating their potential to enhance patient outcomes and reduce the impact of this devastating disease.},
}
@article {pmid39258254,
year = {2024},
author = {Sun, W and Zheng, L and Kang, L and Chen, C and Wang, L and Lu, L and Wang, F},
title = {Comparative analysis of metagenomic and targeted next-generation sequencing for pathogens diagnosis in bronchoalveolar lavage fluid specimens.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1451440},
pmid = {39258254},
issn = {2235-2988},
mesh = {*Bronchoalveolar Lavage Fluid/microbiology/virology ; Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Female ; Male ; Middle Aged ; Adult ; Multiplex Polymerase Chain Reaction/methods ; Aged ; Bacteria/isolation &amp; purification/genetics/classification ; Respiratory Tract Infections/diagnosis/virology/microbiology ; Viruses/isolation &amp; purification/genetics/classification ; Molecular Diagnostic Techniques/methods ; Young Adult ; },
abstract = {BACKGROUND: Although the emerging NGS-based assays, metagenomic next-generation sequencing (mNGS) and targeted next-generation sequencing (tNGS), have been extensively utilized for the identification of pathogens in pulmonary infections, there have been limited studies systematically evaluating differences in the efficacy of mNGS and multiplex PCR-based tNGS in bronchoalveolar lavage fluid (BALF) specimens.<br><br>METHODS: In this study, 85 suspected infectious BALF specimens were collected. Parallel mNGS and tNGS workflows to each sample were performed; then, we comparatively compared their consistency in detecting pathogens. The differential results for clinically key pathogens were confirmed using PCR.<br><br>RESULTS: The microbial detection rates of BALF specimens by the mNGS and tNGS workflows were 95.18% (79/83) and 92.77% (77/83), respectively, with no significant difference. mNGS identified 55 different microorganisms, whereas tNGS detected 49 pathogens. The comparative analysis of mNGS and tNGS revealed that 86.75% (72/83) of the specimens were complete or partial concordance. Particularly, mNGS and tNGS differed significantly in detection rates for some of the human herpesviruses only, including Human gammaherpesvirus 4 (P<0.001), Human betaherpesvirus 7 (P<0.001), Human betaherpesvirus 5 (P<0.05) and Human betaherpesvirus 6 (P<0.01), in which tNGS always had higher detection rates. Orthogonal testing of clinically critical pathogens showed a total coincidence rate of 50% for mNGS and PCR, as well as for tNGS and PCR.<br><br>CONCLUSIONS: Overall, the performance of mNGS and multiplex PCR-based tNGS assays was similar for bacteria and fungi, and tNGS may be superior to mNGS for the detection of DNA viruses. No significant differences were seen between the two NGS assays compared to PCR.},
}
@article {pmid39257939,
year = {2024},
author = {Markam, SS and Raj, A and Kumar, A and Khan, ML},
title = {Microbial biosurfactants: Green alternatives and sustainable solution for augmenting pesticide remediation and management of organic waste.},
journal = {Current research in microbial sciences},
volume = {7},
number = {},
pages = {100266},
pmid = {39257939},
issn = {2666-5174},
abstract = {Pesticide pollution remains a significant environmental challenge, necessitating the exploration of sustainable alternatives. Biosurfactants are a class of unconventional surface-active chemicals that are produced by microorganisms. Biosurfactants have many applications in treating oil spills, emulsifiers, pharmaceuticals, and agriculture. Compared to chemical surfactants, they have benefits such as biodegradability, less toxicity, and a greener option because they are derived from microbes. Biosurfactants have recently been shown to have the potential to speed up pesticide cleanup. Biosurfactants are used in pesticide remediation because of their exceptional foaming ability, high selectivity, and wide range of pH, salinity, and temperature operating windows. Microbial biosurfactants emerged as potential agents for the treatment of organic waste and agricultural residue. This review unfolds the promising realm of microbial biosurfactants as green solutions for environmental sustainability, particularly in agricultural practices, with special reference to pesticide remediation. This article highlights the escalating need for eco-friendly alternatives, paving the way for discussing biosurfactants. Moreover, the articles discuss in detail various advancements in the field of rapid screening of biosurfactants, either using a conventional approach or via advanced instruments such as GC-MS, HPLC, NMR, FTIR, etc. Furthermore, the article unveils the molecular mechanisms and the microbial genes driving biosurfactant synthesis, offering insights into enhancing production efficiency. Moreover, the article explores diverse applications of microbial biosurfactants in sustainable agriculture, ranging from soil remediation to crop protection. The article also highlights the various functions of microbial biosurfactants for enhancing the decomposition and recycling of organic waste and agricultural residues, emphasizing their potential for sustainable waste management strategies. Overall, the review underscores the pivotal role of microbial biosurfactants as green alternatives for addressing pesticide pollution and advancing environmental sustainability.},
}
@article {pmid39257733,
year = {2024},
author = {Rienzi, SCD and Danhof, HA and Forshee, MD and Roberts, A and Britton, RA},
title = {Limosilactobacillus reuteri promotes the expression and secretion of enteroendocrine- and enterocyte-derived hormones.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39257733},
issn = {2692-8205},
support = {F32 AI136404/AI/NIAID NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; T15 LM007093/LM/NLM NIH HHS/United States ; },
abstract = {Observations that intestinal microbes can beneficially impact host physiology have prompted investigations into the therapeutic usage of such microbes in a range of diseases. For example, the human intestinal microbe Limosilactobacillus reuteri strains ATCC PTA 6475 and DSM 17938 are being considered for use for intestinal ailments including colic, infection, and inflammation as well as non-intestinal ailments including osteoporosis, wound healing, and autism spectrum disorder. While many of their beneficial properties are attributed to suppressing inflammatory responses in the gut, we postulated that L. reuteri may also regulate hormones of the gastrointestinal tract to affect physiology within and outside of the gut. To determine if L. reuteri secreted factors impact the secretion of enteric hormones, we treated an engineered jejunal organoid line, NGN3-HIO, which can be induced to be enriched in enteroendocrine cells, with L. reuteri 6475 or 17938 conditioned medium and performed transcriptomics. Our data suggest that these L. reuteri strains affect the transcription of many gut hormones, including vasopressin and luteinizing hormone subunit beta, which have not been previously recognized as being produced in the gut epithelium. Moreover, we find that these hormones appear to be produced in enterocytes, in contrast to canonical gut hormones which are produced in enteroendocrine cells. Finally, we show that L. reuteri conditioned media promotes the secretion of several enteric hormones including serotonin, GIP, PYY, vasopressin, and luteinizing hormone subunit beta. These results support L. reuteri affecting host physiology through intestinal hormone secretion, thereby expanding our understanding of the mechanistic actions of this microbe.},
}
@article {pmid39257028,
year = {2024},
author = {Jotta, VFM and García, GJY and Fonseca, PLC and de Mello Ferreira, A and Azevedo, V and Brenig, B and Góes-Neto, A and Badotti, F},
title = {Taxonomic and functional characterization of biofilms from a photovoltaic panel reveals high genetic and metabolic complexity of the communities.},
journal = {Journal of applied microbiology},
volume = {135},
number = {9},
pages = {},
doi = {10.1093/jambio/lxae231},
pmid = {39257028},
issn = {1365-2672},
support = {//Omics Sciences NETWORK/ ; //CEFET-MG/ ; },
mesh = {*Biofilms/growth &amp; development ; Brazil ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; Metagenomics ; Ferric Compounds/metabolism ; Microbiota ; Minerals/metabolism ; Bioelectric Energy Sources/microbiology ; Iron Compounds ; },
abstract = {AIMS: Biofilms are complex microbial cell aggregates that attach to different surfaces in nature, industrial environments, or hospital settings. In photovoltaic panels (PVs), biofilms are related to significant energy conversion losses. In this study, our aim was to characterize the communities of microorganisms and the genes involved in biofilm formation.<br><br>METHODS AND RESULTS: In this study, biofilm samples collected from a PV system installed in southeastern Brazil were analyzed through shotgun metagenomics, and the microbial communities and genes involved in biofilm formation were investigated. A total of 2030 different genera were identified in the samples, many of which were classified as extremophiles or producers of exopolysaccharides. Bacteria prevailed in the samples (89%), mainly the genera Mucilaginibacter, Microbacterium, Pedobacter, Massilia, and Hymenobacter. The functional annotation revealed >12&#x2009;000 genes related to biofilm formation and stress response. Genes involved in the iron transport and synthesis of c-di-GMP and c-AMP second messengers were abundant in the samples. The pathways related to these components play a crucial role in biofilm formation and could be promising targets for preventing biofilm formation in the PV. In addition, Raman spectroscopy analysis indicated the presence of hematite, goethite, and ferrite, consistent with the mineralogical composition of the regional soil and metal-resistant bacteria.<br><br>CONCLUSIONS: Taken together, our findings reveal that PV biofilms are a promising source of microorganisms of industrial interest and genes of central importance in regulating biofilm formation and persistence.},
}
@article {pmid39256724,
year = {2024},
author = {Gamage, BD and Ranasinghe, D and Sahankumari, A and Malavige, GN},
title = {Metagenomic analysis of colonic tissue and stool microbiome in patients with colorectal cancer in a South Asian population.},
journal = {BMC cancer},
volume = {24},
number = {1},
pages = {1124},
pmid = {39256724},
issn = {1471-2407},
support = {ASP/01/RE/MED/2018/52//University of Sri Jayewardenepura/ ; ASP/01/RE/MED/2018/52//University of Sri Jayewardenepura/ ; },
mesh = {Adult ; Aged ; Female ; Humans ; Male ; Middle Aged ; Bacteria/classification/isolation &amp; purification ; Colon/microbiology ; *Colorectal Neoplasms/microbiology ; *Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Metagenome ; Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; South Asian People ; },
abstract = {BACKGROUND: The gut microbiome is thought to play an important role in the development of colorectal cancer (CRC). However, as the gut microbiome varies widely based on diet, we sought to investigate the gut microbiome changes in patients with CRC in a South Asian population.<br><br>METHODS: The gut microbiome was assessed by 16s metagenomic sequencing targeting the V4 hypervariable region of the bacterial 16S rRNA in stool samples (n&#x2009;=&#x2009;112) and colonic tissue (n&#x2009;=&#x2009;36) in 112 individuals. The cohort comprised of individuals with CRC (n&#x2009;=&#x2009;24), premalignant lesions (n&#x2009;=&#x2009;10), healthy individuals (n&#x2009;=&#x2009;50) and in those with diabetes (n&#x2009;=&#x2009;28).<br><br>RESULTS: Overall, the relative abundances of genus Fusobacterium (p&#x2009;<&#x2009;0.001), Acinetobacter (p&#x2009;<&#x2009;0.001), Escherichia-Shigella (p&#x2009;<&#x2009;0.05) were significantly higher in gut tissue, while Romboutsia (p&#x2009;<&#x2009;0.01) and Prevotella (p&#x2009;<&#x2009;0.05) were significantly higher in stool samples. Bacteroides and Fusobacterium were the most abundant genera found in stool samples in patients with CRC. Patients with pre-malignant lesions had significantly high abundances of Christensenellaceae, Enterobacteriaceae, Mollicutes and Ruminococcaceae (p&#x2009;<&#x2009;0.001) compared to patients with CRC, and healthy individuals. Romboutsia was significantly more abundant (p&#x2009;<&#x2009;0.01) in stool samples in healthy individuals compared to those with CRC and diabetes.<br><br>CONCLUSION: Despite marked differences in the Sri Lankan diet compared to the typical Western diet, Bacteroides and Fusobacterium species were the most abundant in those with CRC, with Prevotella species, being most abundant in many individuals. We believe these results pave the way for possible dietary interventions for prevention of CRC in the South Asian population.},
}
@article {pmid39256682,
year = {2024},
author = {Wu, LH and Hu, CX and Liu, TX},
title = {Metagenomic profiling of gut microbiota in Fall Armyworm (Spodoptera frugiperda) larvae fed on different host plants.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {337},
pmid = {39256682},
issn = {1471-2180},
mesh = {Animals ; *Spodoptera/microbiology/genetics ; *Larva/microbiology ; *Gastrointestinal Microbiome/genetics ; *Metagenomics ; *Zea mays/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Sorghum/microbiology ; Solanum lycopersicum/microbiology ; Capsicum/microbiology ; Metagenome ; },
abstract = {BACKGROUND: The fall armyworm (FAW, Spodoptera frugiperda) is a polyphagous pest known for causing significant crop damage. The gut microbiota plays a pivotal role in influencing the biology, physiology and adaptation of the host. However, understanding of the taxonomic composition and functional characteristics of the gut microbiota in FAW larvae fed on different host plants remains limited.<br><br>METHODS: This study utilized metagenomic sequencing to explore the structure, function and antibiotic resistance genes (ARGs) of the gut microbiota in FAW larvae transferred from an artificial diet to four distinct host plants: maize, sorghum, tomato and pepper.<br><br>RESULTS: The results demonstrated significant variations in gut microbiota structure among FAW larvae fed on different host plants. Firmicutes emerged as the dominant phylum, with Enterococcaceae as the dominant family and Enterococcus as the prominent genus. Notably, Enterococcus casseliflavus was frequently observed in the gut microbiota of FAW larvae across host plants. Metabolism pathways, particularly those related to carbohydrate and amino acid metabolism, played a crucial role in the adaptation of the FAW gut microbiota to different host plants. KEGG orthologs associated with the regulation of the peptide/nickel transport system permease protein in sorghum-fed larvae and the 6-phospho-&#x3b2;-glucosidase gene linked to glycolysis/gluconeogenesis as well as starch and sucrose metabolism in pepper-fed larvae were identified. Moreover, the study identified the top 20 ARGs in the gut microbiota of FAW larvae fed on different host plants, with the maize-fed group exhibiting the highest abundance of vanRC.<br><br>CONCLUSIONS: Our metagenomic sequencing study reveals significant variations in the gut microbiota composition and function of FAW larvae across diverse host plants. These findings underscore the intricate co-evolutionary relationship between hosts and their gut microbiota, suggesting that host transfer profoundly influences the gut microbiota and, consequently, the adaptability and pest management strategies for FAW.},
}
@article {pmid39256599,
year = {2024},
author = {Chen, Y and Zhang, KX and Liu, H and Zhu, Y and Bu, QY and Song, SX and Li, YC and Zou, H and You, XY and Zhao, GP},
title = {Impact of ginsenoside Rb1 on gut microbiome and associated changes in pharmacokinetics in rats.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {21168},
pmid = {39256599},
issn = {2045-2322},
support = {TSBICIP-CXRC-042//Tianjin Synthetic Biotechnology Innovation Capacity Improvement Projects/ ; TSBICIP-CXRC-008//Tianjin Synthetic Biotechnology Innovation Capacity Improvement Projects/ ; E2M9560201//Major Project of Haihe Laboratory of Synthetic Biology/ ; 31200035//National Natural Science Foundation of China/ ; XDC 0110300//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; },
mesh = {*Ginsenosides/pharmacokinetics/pharmacology ; Animals ; *Gastrointestinal Microbiome/drug effects ; Rats ; Male ; *Bacteroides/drug effects ; Rats, Sprague-Dawley ; Glycoside Hydrolases/metabolism ; },
abstract = {Ginsenoside Rb1 exhibits a wide range of biological activities, and gut microbiota is considered the main metabolic site for Rb1. However, the impact of gut microbiota on the pharmacokinetics of Rb1 are still uncertain. In this study, we investigated the gut microbiome changes and the pharmacokinetics after a 30 d Rb1 intervention. Results reveal that the systemic exposure and metabolic clearance rate of Rb1 and Rd were substantially affected after orally supplementing Rb1 (60 mg/kg) to rats. Significant increase in the relative abundance of Bacteroides cellulosilyticus in gut microbiota and specific glycoside hydrolase (GH) families, such as GH2, GH92, and GH20 were observed based on microbiome and metagenomic analysis. Moreover, a robust association was identified between the pharmacokinetic parameters of Rb1 and the relative abundance of specific Bacteroides species, and glycoside hydrolase families. Our study demonstrates that Rb1 administration significantly affects the gut microbiome, revealing a complex relationship between B. cellulosilyticus, key GH families, and Rb1 pharmacokinetics.},
}
@article {pmid39256479,
year = {2024},
author = {Campese, L and Russo, L and Abagnale, M and Alberti, A and Bachi, G and Balestra, C and Bellardini, D and Buondonno, A and Cardini, U and Carotenuto, Y and Checcucci, G and Chiusano, ML and D'Ambra, I and d'Ippolito, G and Di Capua, I and Donnarumma, V and Fontana, A and Furia, M and Galarza-Verkovitch, D and Gallia, R and Labadie, K and Leone, S and Licandro, P and Longo, A and Maselli, M and Merquiol, L and Murano, C and Oliveira, PH and Passarelli, A and Percopo, I and Perdereau, A and Piredda, R and Raffini, F and Roncalli, V and Ruscheweyh, HJ and Russo, E and Saggiomo, M and Santinelli, C and Sarno, D and Sunagawa, S and Tramontano, F and Trano, AC and Uttieri, M and Wincker, P and Zampicinini, G and Casotti, R and Conversano, F and D'Alelio, D and Iudicone, D and Margiotta, F and Montresor, M},
title = {The NEREA Augmented Observatory: an integrative approach to marine coastal ecology.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {989},
pmid = {39256479},
issn = {2052-4463},
mesh = {*Ecosystem ; Plankton ; Metagenome ; Biodiversity ; Metagenomics ; },
abstract = {The NEREA (Naples Ecological REsearch for Augmented observatories) initiative aims to establish an augmented observatory in the Gulf of Naples (GoN), designed to advance the understanding of marine ecosystems through a holistic approach. Inspired by the Tara Oceans expedition and building on the scientific legacy of the MareChiara Long-Term Ecological Research (LTER-MC) site, NEREA integrates traditional physical, chemical, and biological measurements with state-of-the-art methodologies such as metabarcoding and metagenomics. Here we present the first 10 months of NEREA data, collected from April 2019 to January 2020, encompassing physico-chemical parameters, plankton biodiversity (e.g., microscopy and flow cytometry), prokaryotic and eukaryotic metabarcoding, a prokaryotic gene catalogue, and a collection of 3818 prokaryotic Metagenome-Assembled Genomes (MAGs). NEREA's efforts produce a significant volume of multifaceted data, which enhances our understanding of marine ecosystems and promotes the development of scientific hypotheses and ideas.},
}
@article {pmid39256206,
year = {2024},
author = {Ashade, AO and Obayori, OS and Salam, LB and Fashola, MO and Nwaokorie, FO},
title = {Effects of anthropogenic activities on the microbial community diversity of Ologe Lagoon sediment in Lagos State, Nigeria.},
journal = {Environmental monitoring and assessment},
volume = {196},
number = {10},
pages = {918},
pmid = {39256206},
issn = {1573-2959},
mesh = {Nigeria ; *Geologic Sediments/microbiology/chemistry ; *Environmental Monitoring ; *Microbiota ; *Water Pollutants, Chemical/analysis ; Metals, Heavy/analysis ; Anthropogenic Effects ; Bacteria/classification/genetics ; Hydrocarbons/analysis ; },
abstract = {The impact of pollution on the Ologe Lagoon was assessed by comparing physicochemical properties, hydrocarbon concentrations and microbial community structures of the sediments obtained from distinct sites of the lagoon. The locations were the human activity site (OLHAS), industrial-contaminated sites (OLICS) and relatively undisturbed site (OLPS). The physicochemical properties, heavy metal concentrations and hydrocarbon profiles were determined using standard methods. The microbial community structures of the sediments were determined using shotgun next-generation sequencing (NGS), taxonomic profiling was performed using centrifuge and statistical analysis was done using statistical analysis for metagenomics profile (STAMP) and Microsoft Excel. The result showed acidic pH across all sampling points, while the nitrogen content at OLPS was low (7.44 ± 0.085 mg/L) as compared with OLHAS (44.380 ± 0.962 mg/L) and OLICS (59.485 ± 0.827 mg/L). The levels of the cadmium, lead and nickel in the three sites were above the regulatory limits. The gas chromatography flame ionization detector (GC-FID) profile revealed hydrocarbon contaminations with nC14 tetradecane > alpha xylene > nC9 nonane > acenaphthylene more enriched at OLPS. Structurally, the sediments metagenomes consisted of 43 phyla,75 classes each, 165, 161, 166 orders, 986, 927 and 866 bacterial genera and 1476, 1129, 1327 species from OLHAS, OLICS and OLPS, respectively. The dominant phyla in the sediments were Proteobacteria, Firmicutes, Actinobacteria, and Chloroflexi. The principal component ordination (PCO) showed that OLPS microbial community had a total variance of 87.7% PCO1, setting it apart from OLHAS and OLICS. OLICS and OLHAS were separated by PCO2 accounting for 12.3% variation, and the most polluted site is the OLPS.},
}
@article {pmid39255933,
year = {2024},
author = {Kim, Y and Choe, S and Cho, Y and Moon, H and Shin, H and Seo, J and Myung, J},
title = {Biodegradation of poly(butylene adipate terephthalate) and poly(vinyl alcohol) within aquatic pathway.},
journal = {The Science of the total environment},
volume = {953},
number = {},
pages = {176129},
doi = {10.1016/j.scitotenv.2024.176129},
pmid = {39255933},
issn = {1879-1026},
abstract = {Understanding the environmental fate of biodegradable plastics in aquatic systems is crucial, given the alarming amount of plastic waste and microplastic particles transported through aquatic pathways. In particular, there is a need to analyze the biodegradation of commercialized biodegradable plastics upon release from wastewater treatment plants into natural aquatic systems. This study investigates the biodegradation behaviors of poly(butylene adipate terephthalate) (PBAT) and poly(vinyl alcohol) (PVA) in wastewater, freshwater, and seawater. Biodegradation of PBAT and PVA assessed through biochemical oxygen demand (BOD) experiments and microcosm tests revealed that the type of aquatic system governs the biodegradation behaviors of each plastic, with the highest biodegradation rate achieved in wastewater for both PBAT and PVA (25.6 and 32.2 % in 30 d, respectively). Plastic release pathway from wastewater into other aquatic systems simulated by sequential incubation in different microcosms suggested that PBAT exposed to wastewater and freshwater before reaching seawater was more prone to degradation than when directly exposed to seawater. On the other hand, PVA displayed comparable biodegradation rate regardless of whether it was directly exposed to seawater or had passed through other environments beforehand. Metagenome amplicon sequencing of 16S rRNA genes revealed distinct community shifts dependent on the type of plastics in changing environments along the simulated aquatic pathway. Several bacterial species putatively implicated in the biodegradation of PBAT and PVA are discussed. Our findings underscore the significant influence of pollution routes on the biodegradation of PBAT and PVA, highlighting the potential for wastewater treatment to facilitate rapid degradation compared to direct exposure to pristine aquatic environments.},
}
@article {pmid39255566,
year = {2024},
author = {Quan, H and Jia, Y and Zhang, H and Ji, F and Shi, Y and Deng, Q and Hao, T and Khanal, SK and Sun, L and Lu, H},
title = {Insights into the role of electrochemical stimulation on sulfur-driven biodegradation of antibiotics in wastewater treatment.},
journal = {Water research},
volume = {266},
number = {},
pages = {122385},
doi = {10.1016/j.watres.2024.122385},
pmid = {39255566},
issn = {1879-2448},
abstract = {The presence of antibiotics in wastewater poses significant threat to our ecosystems and health. Traditional biological wastewater treatment technologies have several limitations in treating antibiotic-contaminated wastewaters, such as low removal efficiency and poor process resilience. Here, a novel electrochemical-coupled sulfur-mediated biological system was developed for treating wastewater co-contaminated with several antibiotics (e.g., ciprofloxacin (CIP), sulfamethoxazole (SMX), chloramphenicol (CAP)). Superior removal of CIP, SMX, and CAP with efficiencies ranging from 40.6 ± 2.6 % to 98.4 ± 1.6 % was achieved at high concentrations of 1000 μg/L in the electrochemical-coupled sulfur-mediated biological system, whereas the efficiencies ranged from 30.4 ± 2.3 % to 98.2 ± 1.4 % in the control system (without electrochemical stimulation). The biodegradation rates of CIP, SMX, and CAP increased by 1.5∼1.9-folds under electrochemical stimulation compared to the control. The insights into the role of electrochemical stimulation for multiple antibiotics biodegradation enhancement was elucidated through a combination of metagenomic and electrochemical analyses. Results showed that sustained electrochemical stimulation significantly enriched the sulfate-reducing and electroactive bacteria (e.g., Desulfobulbus, Longilinea, and Lentimicrobiumin on biocathode and Geobactor on bioanode), and boosted the secretion of electron transport mediators (e.g., cytochrome c and extracellular polymeric substances), which facilitated the microbial extracellular electron transfer processes and subsequent antibiotics removal in the sulfur-mediated biological system. Furthermore, under electrochemical stimulation, functional genes associated with sulfur and carbon metabolism and electron transfer were more abundant, and the microbial metabolic processes were enhanced, contributing to antibiotics biodegradation. Our study for the first time demonstrated that the synergistic effects of electrochemical-coupled sulfur-mediated biological system was capable of overcoming the limitations of conventional biological treatment processes. This study shed light on the mechanism of enhanced antibiotics biodegradation via electrochemical stimulation, which could be employed in sulfur-mediated bioprocess for treating antibiotic-contaminated wastewaters.},
}
@article {pmid39255397,
year = {2024},
author = {Park, G and Kadyan, S and Hochuli, N and Salazar, G and Laitano, O and Chakrabarty, P and Efron, PA and Zafar, MA and Wilber, A and Nagpal, R},
title = {An Enteric Bacterial Infection Triggers Neuroinflammation and Neurobehavioral Impairment in 3xTg-AD Transgenic Mice.},
journal = {The Journal of infectious diseases},
volume = {230},
number = {Supplement_2},
pages = {S95-S108},
pmid = {39255397},
issn = {1537-6613},
support = {23A02//Florida Department of Health/ ; R01 AG070094/NH/NIH HHS/United States ; R01 AG070094/AG/NIA NIH HHS/United States ; //Foundation/ ; R21 AI166642/AI/NIAID NIH HHS/United States ; 440658//US Department of Agriculture/ ; R01 AI173244/AI/NIAID NIH HHS/United States ; //Infectious Diseases Society of America/ ; //Florida State University/ ; R01AI173244//US Public Health Service/ ; },
mesh = {Animals ; Mice ; *Mice, Transgenic ; *Klebsiella pneumoniae ; *Disease Models, Animal ; *Dysbiosis/microbiology/chemically induced ; *Alzheimer Disease/microbiology ; *Neuroinflammatory Diseases/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Klebsiella Infections/microbiology ; *Blood-Brain Barrier/microbiology ; Brain/pathology/microbiology ; Anti-Bacterial Agents/pharmacology ; Brain-Gut Axis ; Male ; Humans ; },
abstract = {BACKGROUND: Klebsiella pneumoniae is infamous for hospital-acquired infections and sepsis, which have also been linked to Alzheimer disease (AD)-related neuroinflammatory and neurodegenerative impairment. However, its causative and mechanistic role in AD pathology remains unstudied.<br><br>METHODS: A preclinical model of K. pneumoniae enteric infection and colonization is developed in an AD model (3xTg-AD mice) to investigate whether and how K. pneumoniae pathogenesis exacerbates neuropathogenesis via the gut-blood-brain axis.<br><br>RESULTS: K. pneumoniae, particularly under antibiotic-induced dysbiosis, was able to translocate from the gut to the bloodstream by penetrating the gut epithelial barrier. Subsequently, K. pneumoniae infiltrated the brain by breaching the blood-brain barrier. Significant neuroinflammatory phenotype was observed in mice with K. pneumoniae brain infection. K. pneumoniae-infected mice also exhibited impaired neurobehavioral function and elevated total tau levels in the brain. Metagenomic analyses revealed an inverse correlation of K. pneumoniae with gut biome diversity and commensal bacteria, highlighting how antibiotic-induced dysbiosis triggers an enteroseptic "pathobiome" signature implicated in gut-brain perturbations.<br><br>CONCLUSIONS: The findings demonstrate how infectious agents following hospital-acquired infections and consequent antibiotic regimen may induce gut dysbiosis and pathobiome and increase the risk of sepsis, thereby increasing the predisposition to neuroinflammatory and neurobehavioral impairments via breaching the gut-blood-brain barrier.},
}
@article {pmid39254351,
year = {2024},
author = {Wasmund, K and Singleton, C and Dahl Dueholm, MK and Wagner, M and Nielsen, PH},
title = {The predicted secreted proteome of activated sludge microorganisms indicates distinct nutrient niches.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0030124},
doi = {10.1128/msystems.00301-24},
pmid = {39254351},
issn = {2379-5077},
abstract = {In wastewater treatment plants (WWTPs), complex microbial communities process diverse chemical compounds from sewage. Secreted proteins are critical because many are the first to interact with or degrade external (macro)molecules. To better understand microbial functions in WWTPs, we predicted secreted proteomes of WWTP microbiota from more than 1,000 high-quality metagenome-assembled genomes (MAGs) from 23 Danish WWTPs with biological nutrient removal. Focus was placed on examining secreted catabolic exoenzymes that target major classes of macromolecules. We demonstrate that Bacteroidota has a high potential to digest complex polysaccharides, but also proteins and nucleic acids. Poorly understood activated sludge members of Acidobacteriota and Gemmatimonadota also have high capacities for extracellular polysaccharide digestion. Secreted nucleases are encoded by 61% of MAGs indicating an importance for extracellular DNA and/or RNA digestion in WWTPs. Secreted lipases were the least common macromolecule-targeting enzymes predicted, encoded mainly by Gammaproteobacteria and Myxococcota. In contrast, diverse taxa encode extracellular peptidases, indicating that proteins are widely used nutrients. Diverse secreted multi-heme cytochromes suggest capabilities for extracellular electron transfer by various taxa, including some Bacteroidota that encode undescribed cytochromes with >100 heme-binding motifs. Myxococcota have exceptionally large secreted protein complements, probably related to predatory lifestyles and/or complex cell cycles. Many Gammaproteobacteria MAGs (mostly former Betaproteobacteria) encode few or no secreted hydrolases, but many periplasmic substrate-binding proteins and ABC- and TRAP-transporters, suggesting they are mostly sustained by small molecules. Together, this study provides a comprehensive overview of how WWTPs microorganisms interact with the environment, providing new insights into their functioning and niche partitioning.IMPORTANCEWastewater treatment plants (WWTPs) are critical biotechnological systems that clean wastewater, allowing the water to reenter the environment and limit eutrophication and pollution. They are also increasingly important for the recovery of resources. They function primarily by the activity of microorganisms, which act as a "living sponge," taking up and transforming nutrients, organic material, and pollutants. Despite much research, many microorganisms in WWTPs are uncultivated and poorly characterized, limiting our understanding of their functioning. Here, we analyzed a large collection of high-quality metagenome-assembled genomes from WWTPs for encoded secreted enzymes and proteins, with special emphasis on those used to degrade organic material. This analysis showed highly distinct secreted proteome profiles among different major phylogenetic groups of microorganisms, thereby providing new insights into how different groups function and co-exist in activated sludge. This knowledge will contribute to a better understanding of how to efficiently manage and exploit WWTP microbiomes.},
}
@article {pmid39254336,
year = {2024},
author = {Jung, D and Park, S and Kurban, D and Dufour, S and Ronholm, J},
title = {The occurrence of Aerococcus urinaeequi and non-aureus staphylococci in raw milk negatively correlates with Escherichia coli clinical mastitis.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0036224},
doi = {10.1128/msystems.00362-24},
pmid = {39254336},
issn = {2379-5077},
abstract = {Escherichia coli is a common environmental pathogen associated with clinical mastitis (CM) in dairy cattle. There is an interest in optimizing the udder microbiome to increase the resistance of dairy cattle to E. coli CM; however, the details of which members of the healthy udder microbiome may play a role in antagonizing E. coli are unknown. In this study, we characterized the bacterial community composition in raw milk collected from quarters of lactating Holstein dairy cows that developed E. coli CM during lactation, including milk from both healthy and diseased quarters (n = 1,172). The milk microbiome from infected quarters was compared before, during, and after CM. A combination of 16S rRNA gene amplicon and metagenomic sequencing was used generate data sets with a high level of both depth and breadth. The microbial diversity present in raw milk significantly decreased in quarters experiencing E. coli CM, indicating that E. coli displaces other members of the microbiome. However, the diversity recovered very rapidly after infection. Two genera, Staphylococcus and Aerococcus, and the family Oscillospiraceae were significantly more abundant in healthy quarters with low inflammation. Species of these genera, Staphylococcus auricularis, Staphylococcus haemolyticus, and Aerocussus urinaeequi, were identified by metagenomics. Thus, these species are of interest for optimizing the microbiome to discourage E. coli colonization without triggering inflammation.IMPORTANCEIn this study, we show that E. coli outcompetes and displaces several members of the udder microbiome during CM, but that microbial diversity recovers post-infection. In milk from quarters which remained healthy, the community composition was often highly dominated by S. auricularis, S. haemolyticus, A. urinaeequi, and S. marcescens without increases in somatic cell count (SCC). Community dominance by these organisms, without inflammation, could indicate that these species might have potential as prophylactic probiotics which could contribute to colonization resistance and prevent future instances of E. coli CM.},
}
@article {pmid39254265,
year = {2024},
author = {Anandakumar, H and Rauch, A and Wimmer, MI and Yarritu, A and Koch, G and McParland, V and Bartolomaeus, H and Wilck, N},
title = {Segmental patterning of microbiota and immune cells in the murine intestinal tract.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2398126},
pmid = {39254265},
issn = {1949-0984},
mesh = {Animals ; *Gastrointestinal Microbiome ; Mice ; *Mice, Inbred C57BL ; *Bacteria/classification/genetics/isolation &amp; purification/immunology ; Intestines/microbiology/immunology/cytology ; Metagenomics ; Germ-Free Life ; Female ; T-Lymphocyte Subsets/immunology ; Male ; Intestinal Mucosa/microbiology/immunology/cytology ; },
abstract = {The intestine exhibits distinct characteristics along its length, with a substantial immune cell reservoir and diverse microbiota crucial for maintaining health. This study investigates how anatomical location and regional microbiota influence intestinal immune cell abundance. Using conventionally colonized and germ-free mice, segment-specific immune cell composition and microbial communities were assessed. Metagenomic sequencing analyzed microbiome variations, while flow cytometry and immunofluorescence examined immune cell composition. Microbiome composition varied significantly along the intestine, with diversity and abundance increasing from upper to lower segments. Immune cells showed distinct segment-specific patterning influenced by microbial colonization and localization. T cell subsets displayed varied dependence on microbiome presence and anatomical location. This study highlights locoregional differences in intestinal immune cell and microbiome composition, identifying immune subsets susceptible to microbiota presence. The findings provide context for understanding immune cell alterations in disease models.},
}
@article {pmid39254230,
year = {2024},
author = {Qi, Q and Ning, S and Guo, X and Zhao, J and Tian, R and Gui, H and He, JS and Wang, H and Zhang, Z and Konstantinidis, KT and Gao, Q and Wang, Y and Li, S and Zhao, W and Yang, Y and Zhou, J},
title = {More sensitive microbial responses to the interactive effects of warming and altered precipitation in subsoil than topsoil of an alpine grassland ecosystem.},
journal = {Global change biology},
volume = {30},
number = {9},
pages = {e17487},
doi = {10.1111/gcb.17487},
pmid = {39254230},
issn = {1365-2486},
support = {//the CAS Youth Interdisciplinary Team/ ; 32161123002//National Natural Science Foundation of China/ ; 42277213//National Natural Science Foundation of China/ ; 41907209//National Natural Science Foundation of China/ ; 41877048//National Natural Science Foundation of China/ ; 32130065//National Natural Science Foundation of China/ ; 2019QZKK0503//the Second Tibetan Plateau Scientific Expedition and Research Program/ ; },
mesh = {*Soil Microbiology ; *Grassland ; *Climate Change ; *Rain ; *Carbon Cycle ; *Soil/chemistry ; Tibet ; Carbon/analysis/metabolism ; Global Warming ; Bacteria/genetics/classification ; },
abstract = {Subsoil is a large organic carbon reservoir, storing more than half of the total soil organic carbon (SOC) globally. Conventionally, subsoil is assumed to not be susceptible to climate change, but recent studies document that climate change could significantly alter subsoil carbon cycling. However, little is known about subsoil microbial responses to the interactive effects of climate warming and altered precipitation. Here, we investigated carbon cycling and associated microbial responses in both subsoil (30-40 cm) and topsoil (0-10 cm) in a Tibetan alpine grassland over 4 years of warming and altered precipitation. Compared to the unchanged topsoil carbon (β = .55, p = .587), subsoil carbon exhibited a stronger response to the interactive effect of warming and altered precipitation (β = 2.04, p = .021), that is, warming decreased subsoil carbon content by 28.20% under decreased precipitation while warming increased subsoil carbon content by 18.02% under increased precipitation.Furthermore, 512 metagenome-assembled genomes (MAGs) were recovered, including representatives of phyla with poor genomic representation. Compared to only one changed topsoil MAG, 16 subsoil MAGs were significantly affected by altered precipitation, and 5 subsoil MAGs were significantly affected by the interactive effect of warming and precipitation. More than twice as many populations whose MAG abundances correlated significantly with the variations of carbon content, components and fluxes were observed in the subsoil than topsoil, suggesting their potential contribution in mediating subsoil carbon cycling. Collectively, our findings highlight the more sensitive responses of specific microbial lineages to the interactive effects of warming and altered precipitation in the subsoil than topsoil, and provide key information for predicting subsoil carbon cycling under future climate change scenarios.},
}
@article {pmid39254049,
year = {2024},
author = {Harris, RM and Pace, F and Kuntz, TM and Morgan, XC and Hyland, P and Summers, K and McDermott, E and Blumen, K and Watnick, PI},
title = {Testosterone treatment impacts the intestinal microbiome of transgender individuals.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0055724},
doi = {10.1128/msphere.00557-24},
pmid = {39254049},
issn = {2379-5042},
abstract = {Medical modulation of sex hormone levels is a cornerstone of treatment for many conditions that impact well-being, including cancer, fertility/infertility, gender dysphoria, and chronic metabolic diseases such as diabetes and obesity. The microbial residents of the intestine, known as the microbiota, interact with sex hormones in the intestine, and there is correlative evidence that this interaction is bidirectional. Based on these published findings, we hypothesized that transgender individuals receiving exogenous testosterone as part of their gender-affirming medical treatment might undergo changes in their intestinal microbiome. To test this, we collected 26 stool samples from nine individuals before and up to 8 months after initiation of treatment with exogenous testosterone and subjected these samples to metagenomic analysis. While no species were significantly associated with the duration of testosterone therapy, pathways that generate glutamate increased in abundance, while those that consume glutamate decreased. Glutamate is a precursor of arginine, and testosterone is known to increase levels of arginine and its metabolites in the plasma. We hypothesize that testosterone increases the uptake of glutamate by enterocytes, thus decreasing access of the microbiota to this amino acid. While this pilot study establishes the impact of testosterone therapy on the intestinal microbiome, a more comprehensive study is necessary to establish the impact of testosterone-driven metagenomic shifts on the stool metatranscriptome, the stool metabolome, and the plasma metabolome.IMPORTANCEThe human intestine is inhabited by a large community of microbes known as the microbiome. Members of the microbiome consume the diet along with their human host. Thus, the metabolomes of the host and microbe are intricately linked. Testosterone alters the plasma metabolome. In particular, plasma levels of arginine and its metabolites and testosterone are positively correlated. To investigate the impact of exogenous testosterone on the microbiome, we analyzed the stool metagenomes of transgender individuals before and after the initiation of testosterone treatment. In this pilot project, we found a modest impact on the microbiome community structure but an increase in the abundance of metabolic pathways that generate glutamate and spare glutamate consumption. We propose that the host uses glutamate to generate arginine, decreasing the amount available for the microbiome.},
}
@article {pmid39253815,
year = {2024},
author = {Wimmer, MI and Bartolomaeus, H and Anandakumar, H and Chen, CY and Vecera, V and Kedziora, S and Kamboj, S and Schumacher, F and Pals, S and Rauch, A and Meisel, J and Potapenko, O and Yarritu, A and Bartolomaeus, TUP and Samaan, M and Thiele, A and Stürzbecher, L and Geisberger, SY and Kleuser, B and Oefner, PJ and Haase, N and Löber, U and Gronwald, W and Forslund-Startceva, SK and Müller, DN and Wilck, N},
title = {Metformin modulates microbiota and improves blood pressure and cardiac remodeling in a rat model of hypertension.},
journal = {Acta physiologica (Oxford, England)},
volume = {},
number = {},
pages = {e14226},
doi = {10.1111/apha.14226},
pmid = {39253815},
issn = {1748-1716},
support = {//Deutsche Forschungsgemeinschaft/ ; //Deutsches Zentrum f&#xfc;r Herz-Kreislaufforschung/ ; },
abstract = {AIMS: Metformin has been attributed to cardiovascular protection even in the absence of diabetes. Recent observations suggest that metformin influences the gut microbiome. We aimed to investigate the influence of metformin on the gut microbiota and hypertensive target organ damage in hypertensive rats.<br><br>METHODS: Male double transgenic rats overexpressing the human renin and angiotensinogen genes (dTGR), a model of angiotensin II-dependent hypertension, were treated with metformin (300&#x2009;mg/kg/day) or vehicle from 4 to 7&#x2009;weeks of age. We assessed gut microbiome composition and function using shotgun metagenomic sequencing and measured blood pressure via radiotelemetry. Cardiac and renal organ damage and inflammation were evaluated by echocardiography, histology, and flow cytometry.<br><br>RESULTS: Metformin treatment increased the production of short-chain fatty acids (SCFA) acetate and propionate in feces without altering microbial composition and diversity. It significantly reduced systolic and diastolic blood pressure and improved cardiac function, as measured by end-diastolic volume, E/A, and stroke volume despite increased cardiac hypertrophy. Metformin reduced cardiac inflammation by lowering macrophage infiltration and shifting macrophage subpopulations towards a less inflammatory phenotype. The observed improvements in blood pressure, cardiac function, and inflammation correlated with fecal SCFA levels in dTGR. In&#xa0;vitro, acetate and propionate altered M1-like gene expression in macrophages, reinforcing anti-inflammatory effects. Metformin did not affect hypertensive renal damage or microvascular structure.<br><br>CONCLUSION: Metformin modulated the gut microbiome, increased SCFA production, and ameliorated blood pressure and cardiac remodeling in dTGR. Our findings confirm the protective effects of metformin in the absence of diabetes, highlighting SCFA as a potential mediators.},
}
@article {pmid39253787,
year = {2024},
author = {Cheng, S and Gong, X and Xue, W and Kardol, P and Delgado-Baquerizo, M and Ling, N and Chen, X and Liu, M},
title = {Evolutionarily conserved core microbiota as an extended trait in nitrogen acquisition strategy of herbaceous species.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.20118},
pmid = {39253787},
issn = {1469-8137},
support = {42077047//National Foundation of Sciences in China/ ; lzujbky-2022-ct04//Fundamental Research Funds for the Central University of China/ ; 2021YFD1700202//National Key R&amp;D program/ ; },
abstract = {Microbiota have co-evolved with plants over millions of years and are intimately linked to plants, ranging from symbiosis to pathogenesis. However, our understanding of the existence of a shared core microbiota across phylogenetically diverse plants remains limited. A common garden field experiment was conducted to investigate the rhizosphere microbial communities of phylogenetically contrasting herbaceous families. Through a combination of metagenomic sequencing, analysis of plant economic traits, and soil biochemical properties, we aimed to elucidate the eco-evolutionary role of the core rhizosphere microbiota in light of plant economic strategies. We identified a conserved core microbiota consisting of 278 taxa that was closely associated with the phylogeny of the plants studied. This core microbiota actively participated in multiple nitrogen metabolic processes and showed a strong correlation with the functional potential of rhizosphere nitrogen cycling, thereby serving as an extended trait in the plant nitrogen acquisition. Furthermore, our examination of simulated species loss revealed the crucial role of the core microbiota in maintaining the rhizosphere community's network stability. Our study highlighted that the core microbiota, which exhibited a phylogenetically conserved association with plants, potentially represented an extension of the plant phenotype and played an important role in nitrogen acquisition. These findings held implications for the utilization of microbiota-mediated plant functions.},
}
@article {pmid39253606,
year = {2024},
author = {Qin, Y and Zou, X and Jin, Y and Li, J and Cai, Q},
title = {Cryptococcus Neoformans Osteomyelitis of the Right Ankle Diagnosed by Metagenomic Next-Generation Sequencing in a HIV-Negative Patient with Tuberculous Lymphadenitis and Pulmonary Tuberculosis: A Case Report and Recent Literature Review.},
journal = {Infection and drug resistance},
volume = {17},
number = {},
pages = {3805-3812},
pmid = {39253606},
issn = {1178-6973},
abstract = {AIM: Cryptococcus neoformans osteomyelitis coupled with tuberculosis and tuberculous lymphadenitis, is a rare occurrence in clinical. Diagnostic challenges arise due to the clinical radiological similarity of this condition to other lung infections and the limited and sensitive nature of traditional approaches. Here, we present a case of co-infection diagnosed using Metagenomic Next-Generation Sequencing, highlighting the effectiveness of advanced genomic techniques in such complex scenarios.<br><br>CASE PRESENTATION: We present a case of a 67-year-old female infected with cryptococcal osteomyelitis and presented with swelling and pain in the right ankle. Following a biopsy of the right ankle joint, Metagenomic Next-Generation Sequencing (mNGS) of the biopsy tissue revealed Cryptococcus neoformans infection. Positive results for Cryptococcus capsular antigen and pathological findings confirmed the presence of Cryptococcus neoformans. The patient underwent surgical debridement, coupled with oral fluconazole treatment (300mg/day), leading to the resolution of symptoms.<br><br>CONCLUSION: Cryptococcus neoformans is an uncommon cause of ankle infection. Metagenomic Next-Generation Sequencing (mNGS) serves as a valuable diagnostic tool, aiding clinicians in differentiating cryptococcal osteomyelitis from other atypical infections.},
}
@article {pmid39253579,
year = {2024},
author = {Wang, X and Yang, J and Ren, B and Yang, G and Liu, X and Xiao, R and Ren, J and Zhou, F and You, L and Zhao, Y},
title = {Comprehensive multi-omics profiling identifies novel molecular subtypes of pancreatic ductal adenocarcinoma.},
journal = {Genes &amp; diseases},
volume = {11},
number = {6},
pages = {101143},
pmid = {39253579},
issn = {2352-3042},
abstract = {Pancreatic cancer, a highly fatal malignancy, is predicted to rank as the second leading cause of cancer-related death in the next decade. This highlights the urgent need for new insights into personalized diagnosis and treatment. Although molecular subtypes of pancreatic cancer were well established in genomics and transcriptomics, few known molecular classifications are translated to guide clinical strategies and require a paradigm shift. Notably, chronically developing and continuously improving high-throughput technologies and systems serve as an important driving force to further portray the molecular landscape of pancreatic cancer in terms of epigenomics, proteomics, metabonomics, and metagenomics. Therefore, a more comprehensive understanding of molecular classifications at multiple levels using an integrated multi-omics approach holds great promise to exploit more potential therapeutic options. In this review, we recapitulated the molecular spectrum from different omics levels, discussed various subtypes on multi-omics means to move one step forward towards bench-to-beside translation of pancreatic cancer with clinical impact, and proposed some methodological and scientific challenges in store.},
}
@article {pmid39253412,
year = {2024},
author = {Ginnan, NA and Custódio, V and Gopaulchan, D and Ford, N and Salas-González, I and Jones, DD and Wells, DM and Moreno, &#xc2; and Castrillo, G and Wagner, MR},
title = {Persistent legacy effects on soil metagenomes facilitate plant adaptive responses to drought.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.08.26.609769},
pmid = {39253412},
issn = {2692-8205},
abstract = {Both chronic and acute drought alter the composition and physiology of soil microbiomes, with implications for globally important processes including carbon cycling and plant productivity. When water is scarce, selection favors microbes with thicker peptidoglycan cell walls, sporulation ability, and constitutive osmolyte production (Schimel, Balser, and Wallenstein 2007)-but also the ability to degrade complex plant-derived polysaccharides, suggesting that the success of plants and microbes during drought are inextricably linked. However, communities vary enormously in their drought responses and subsequent interactions with plants. Hypothesized causes of this variation in drought resilience include soil texture, soil chemistry, and historical precipitation patterns that shaped the starting communities and their constituent species (Evans, Allison, and Hawkes 2022). Currently, the physiological and molecular mechanisms of microbial drought responses and microbe-dependent plant drought responses in diverse natural soils are largely unknown (de Vries et al. 2023). Here, we identify numerous microbial taxa, genes, and functions that characterize soil microbiomes with legacies of chronic water limitation. Soil microbiota from historically dry climates buffered plants from the negative effects of subsequent acute drought, but only for a wild grass species native to the same region, and not for domesticated maize. In particular, microbiota with a legacy of chronic water limitation altered the expression of a small subset of host genes in crown roots, which mediated the effect of acute drought on transpiration and intrinsic water use efficiency. Our results reveal how long-term exposure to water stress alters soil microbial communities at the metagenomic level, and demonstrate the resulting "legacy effects" on neighboring plants in unprecedented molecular and physiological detail.},
}
@article {pmid39253328,
year = {2024},
author = {Gao, Z and Zheng, W and Zhang, M and Gao, Y and Huang, J and Chen, X and Dai, Z and Song, Z and Feng, J and Cao, Q and Jin, Y},
title = {Metagenomic next-generation sequencing promotes pathogen detection over culture in joint infections with previous antibiotic exposure.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1388765},
pmid = {39253328},
issn = {2235-2988},
mesh = {Humans ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; Male ; Female ; Middle Aged ; Aged ; *Synovial Fluid/microbiology ; *Bacteria/genetics/isolation &amp; purification/classification/drug effects ; Sensitivity and Specificity ; Adult ; Arthritis, Infectious/microbiology/diagnosis/drug therapy ; },
abstract = {OBJECTIVE: To investigate the diagnostic value of metagenomic next-generation sequencing (mNGS) in detecting pathogens from joint infection (JI) synovial fluid (SF) samples with previous antibiotic exposure.<br><br>METHODS: From January 2019 to January 2022, 59 cases with suspected JI were enrolled. All cases had antibiotic exposure within 2 weeks before sample collection. mNGS and conventional culture were performed on SF samples. JI was diagnosed based on history and clinical symptoms in conjunction with MSIS criteria. The diagnostic values, including sensitivity, specificity, positive/negative predictive values (PPV/NPV), and accuracy, were in comparison with mNGS and culture.<br><br>RESULTS: There were 47 of the 59 cases diagnosed with JI, while the remaining 12 were diagnosed with non-infectious diseases. The sensitivity of mNGS was 68.1%, which was significantly higher than that of culture (25.5%, p<0.01). The accuracy of mNGS was significantly higher at 71.2% compared to the culture at 39.0% (p <0.01). Eleven pathogenic strains were detected by mNGS but not by microbiological culture, which included Staphylococcus lugdunensis, Staphylococcus cohnii, Finegoldia magna, Enterococcus faecalis, Staphylococcus saprophytics, Escherichia coli, Salmonella enterica, Pseudomonas aeruginosa, Acinetobacter pittii, Brucella ovis, andCoxiella burnetii. Antibiotic therapy was adjusted based on the mNGS results in 32 (68.1%) patients, including 12 (25.5%) and 20 (42.6%) patients, in whom treatment was upgraded and changed, respectively. All JI patients underwent surgery and received subsequent antibiotic therapy. They were followed up for an average of 23 months (20-27 months), and the success rate of treatment was 89.4%. Out of the 33 patients who had positive results for pathogens, reoperation was performed in 1 case (3.03%), while out of the 14 cases with negative results for both mNGS and cultures, reoperation was performed in 4 cases (28.6%).<br><br>CONCLUSIONS: mNGS has advantages over conventional culture in detecting pathogens in SF samples from JI patients previously treated with antibiotics, potentially improving clinical outcomes.},
}
@article {pmid39253237,
year = {2024},
author = {Zhuang, L and Zhu, C and Ma, J and Zhu, D and Zhu, H and Zhong, S and Liu, X and Wang, Z and Yang, Z and Zhang, W and Ding, R and Chen, D and Zheng, S},
title = {Predictive performance of Metagenomic Next Generation Sequencing in early detection of post-liver transplantation infections.},
journal = {Heliyon},
volume = {10},
number = {16},
pages = {e36405},
pmid = {39253237},
issn = {2405-8440},
abstract = {OBJECTIVE: To evaluate the predictive performance of metagenomic next-generation sequencing (mNGS) in identifying and predicting pulmonary infections following liver transplantation and to investigate its association with patient outcomes within the initial four-week post-transplantation period.<br><br>METHODS: We retrospectively analyzed 41 liver transplant patients with suspected pulmonary infections from August 2022 to May 2023. Bronchoalveolar lavage fluid (BALF) samples were collected on the first postoperative day for metagenomic next generation sequencing (mNGS) and culture. The predictive capability of mNGS for subsequent infections was assessed by monitoring inflammatory biomarkers and comparing the detection rates with culture methods. Real-time Polymerase Chain Reaction (Rt-PCR) was used to monitor Human betaherpesvirus 5 (CMV) and Human parvovirus B19 (B19) weekly during a four-week postoperative period. Inflammatory biomarkers and blood coagulation function were evaluated on specific days throughout the first, third, fifth, and during four weeks following surgery. The study was conducted until August 2023 to evaluate the patients' prognostic survival outcome, classifying them into groups based on the mortality and survival.<br><br>RESULTS: The analysis included a total of 41 patients, comprising 32 males and 9 females, with an average age of 52 (47, 63) years. Within one week after liver transplantation, there were 7 cases of bacterial infections, 5 cases of fungal infections, 19 cases of mixed infections, 8 cases without any infection, and 2 cases with unidentified pathogen-associated infections. mNGS successfully predicted 39 (72&#xa0;%) strains of pathogens, while culture-based methods only detected 28 (52&#xa0;%) strains. Among the 8 patients diagnosed as non-infected, culture methods identified positive results in 4 cases (50&#xa0;%), whereas mNGS yielded positive results in 7 cases (87.5&#xa0;%). The detection rates of CMV and B19 by Rt-PCR within 4 weeks after liver transplantation were 61&#xa0;% and 17&#xa0;%, respectively (25/41, 7/41) among the patients. During the study period, a total of 9 patients succumbed while 32 patients survived. The death group and the survival group exhibited significant differences in CRP, HGB, and INR levels at specific monitoring time points. The proportion of CMV detection in blood was significantly higher in the death group compared to the surviving group. Elevated CRP level was identified as a prognostic risk factor.<br><br>CONCLUSIONS: Despite the presence of false positives, mNGS still presents a potential advantage in predicting pulmonary infection pathogens following liver transplantation. Furthermore, the levels of CRP and CMV carrier status within four weeks post-surgery exhibit significant associations with patient survival and prognosis.},
}
@article {pmid39253087,
year = {2024},
author = {Huang, Z and Hu, B and Li, J and Feng, M and Wang, Z and Huang, F and Xu, H and Liu, L and Shang, W},
title = {Metagenomic versus targeted next-generation sequencing for detection of microorganisms in bronchoalveolar lavage fluid among renal transplantation recipients.},
journal = {Frontiers in immunology},
volume = {15},
number = {},
pages = {1443057},
pmid = {39253087},
issn = {1664-3224},
mesh = {Humans ; *Kidney Transplantation/adverse effects ; *Bronchoalveolar Lavage Fluid/microbiology ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Middle Aged ; Male ; Female ; Adult ; Bacteria/isolation &amp; purification/genetics ; Transplant Recipients ; Aged ; Fungi/isolation &amp; purification/genetics ; },
abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS), which provides untargeted and unbiased pathogens detection, has been extensively applied to improve diagnosis of pulmonary infection. This study aimed to compare the clinical performance between mNGS and targeted NGS (tNGS) for microbial detection and identification in bronchoalveolar lavage fluid (BALF) from kidney transplantation recipients (KTRs).<br><br>METHODS: BALF samples with microbiological results from mNGS and conventional microbiological test (CMT) were included. For tNGS, samples were extracted, amplified by polymerase chain reaction with pathogen-specific primers, and sequenced on an Illumina Nextseq.<br><br>RESULTS: A total of 99 BALF from 99 KTRs, among which 93 were diagnosed as pulmonary infection, were analyzed. Compared with CMT, both mNGS and tNGS showed higher positive rate and sensitivity (p<0.001) for overall, bacterial and fungal detection. Although the positive rate for mNGS and tNGS was comparable, mNGS significantly outperformed tNGS in sensitivity (100% vs. 93.55%, p<0.05), particularly for bacteria and virus (p<0.001). Moreover, the true positive rate for detected microbes of mNGS was superior over that of tNGS (73.97% vs. 63.15%, p<0.05), and the difference was also significant when specific for bacteria (94.59% vs. 64.81%, p<0.001) and fungi (93.85% vs. 72.58%, p<0.01). Additionally, we found that, unlike most microbes such as SARS-CoV-2, Aspergillus, and EBV, which were predominantly detected from recipients who underwent surgery over 3 years, Torque teno virus (TTV) were principally detected from recipients within 1-year post-transplant, and as post-transplantation time increased, the percentage of TTV positivity declined.<br><br>CONCLUSION: Although tNGS was inferior to mNGS owing to lower sensitivity and true positive rate in identifying respiratory pathogens among KTRs, both considerably outperformed CMT.},
}
@article {pmid39252839,
year = {2024},
author = {Murovec, B and Deutsch, L and Stres, B},
title = {Predictive modeling of colorectal cancer using exhaustive analysis of microbiome information layers available from public metagenomic data.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1426407},
pmid = {39252839},
issn = {1664-302X},
abstract = {This study aimed to compare the microbiome profiles of patients with colorectal cancer (CRC, n = 380) and colorectal adenomas (CRA, n = 110) against generally healthy participants (n = 2,461) from various studies. The overarching objective was to conduct a real-life experiment and develop a robust machine learning model applicable to the general population. A total of 2,951 stool samples underwent a comprehensive analysis using the in-house MetaBakery pipeline. This included various data matrices such as microbial taxonomy, functional genes, enzymatic reactions, metabolic pathways, and predicted metabolites. The study found no statistically significant difference in microbial diversity among individuals. However, distinct clusters were identified for healthy, CRC, and CRA groups through linear discriminant analysis (LDA). Machine learning analysis demonstrated consistent model performance, indicating the potential of microbiome layers (microbial taxa, functional genes, enzymatic reactions, and metabolic pathways) as prediagnostic indicators for CRC and CRA. Notable biomarkers on the taxonomy level and microbial functionality (gene families, enzymatic reactions, and metabolic pathways) associated with CRC were identified. The research presents promising avenues for practical clinical applications, with potential validation on external clinical datasets in future studies.},
}
@article {pmid39252828,
year = {2024},
author = {Ng, CWW and Yan, WH and Xia, YT and Tsim, KWK and To, JCT},
title = {Plant growth-promoting rhizobacteria enhance active ingredient accumulation in medicinal plants at elevated CO2 and are associated with indigenous microbiome.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1426893},
pmid = {39252828},
issn = {1664-302X},
abstract = {INTRODUCTION: Plant growth-promoting rhizobacteria (PGPR) and elevated CO2 (eCO2) have demonstrated their individual potential to enhance plant yield and quality through close interaction with rhizosphere microorganisms and plant growth. However, the efficacy of PGPR under eCO2 on rhizosphere microbiome and, ultimately, plant yield and active ingredient accumulation are not yet fully understood.<br><br>METHODS: This study investigated how the medicinal plant Pseudostellaria heterophylla (P. heterophylla) and its rhizosphere microbes respond to PGPR (Bacillus subtilis and Pseudomonas fluorescens) at eCO2 (1,000&#x2009;ppm).<br><br>RESULTS AND DISCUSSION: It was found that the yield and active ingredient polysaccharides accumulation in the tuber of P. heterophylla were significantly increased by 38 and 253%, respectively. This promotion has been associated with increased root development and changes in the indigenous microbial community. Metagenomics analysis revealed a significant reduction in pathogenic Fusarium abundance in the rhizosphere. Potential biocontrol bacteria Actinobacteria and Proteobacteria were enriched, especially the genera Bradyrhizobium and Rhodanobacter. The reshaping of the rhizosphere microbiome was accompanied by the upregulation of biological pathways related to metabolite biosynthesis in the rhizosphere. These modifications were related to the promotion of the growth and productivity of P. heterophylla. Our findings highlighted the significant role played by PGPR in medicinal plant yield and active ingredient accumulation when exposed to eCO2.},
}
@article {pmid39252782,
year = {2024},
author = {Tan, JH and Liew, KJ and Goh, KM},
title = {Dataset of 313 metagenome-assemble genomes from streamer hot spring water.},
journal = {Data in brief},
volume = {56},
number = {},
pages = {110829},
pmid = {39252782},
issn = {2352-3409},
abstract = {This data report presents prokaryotic metagenome-assembled genomes (MAGs) from a hot spring stream with temperatures between 64 and 100°C. The stream water was filtered and the extracted total DNA was sequenced using the Illumina HiSeq 2500 platform. Approximately 80 Gb of raw data were generated, which were subsequently assembled using MEGAHIT v1.2.9. The MAGs were generated using MetaWRAP with binning approaches of MetaBAT2, CONCOCT and MaxBin2. We constructed 25 medium-quality and 24 high-quality archaeal MAGs, and 152 medium-quality and 112 high-quality bacterial MAGs. The fasta files of these MAGs are available in the NCBI database as well as Mendeley Data. Major phyla identified include Bacteroidota, Chloroflexota, Desulfobacterota, Firmicutes, Patescibacteria, Proteobacteria, Spirochaetota, Verrucomicrobiota, Armatimonadota, Nitrospirota, Acidobacteriota, Elusimicrobiota, Planctomycetota, Candidate division WOR-3, Aquificota, Thermoproteota, and Micrarchaeota. This dataset is valuable for studies on thermophilic genomes, reconstruction of biochemical pathways and gene discovery.},
}
@article {pmid39252128,
year = {2024},
author = {Wu, H and Li, A and Zhang, H and Li, S and Yang, C and Lv, H and Yao, Y},
title = {Microbial mechanisms for higher hydrogen production in anaerobic digestion at constant temperature versus gradient heating.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {170},
pmid = {39252128},
issn = {2049-2618},
mesh = {*Hydrogen/metabolism ; *Lignin/metabolism ; Anaerobiosis ; Hot Temperature ; Cellulose/metabolism ; Polysaccharides/metabolism ; Metagenomics/methods ; Temperature ; Bacteria/metabolism/classification/genetics ; },
abstract = {BACKGROUND: Clean energy hydrogen (H2) produced from abundant lignocellulose is an alternative to fossil energy. As an essential influencing factor, there is a lack of comparison between constant temperatures (35, 55 and 65 °C) and gradient heating temperature (35 to 65 °C) on the H2 production regulation potential from lignocellulose-rich straw via high-solid anaerobic digestion (HS-AD). More importantly, the microbial mechanism of temperature regulating H2 accumulation needs to be investigated.<br><br>RESULTS: Constant 65&#xa0;&#xb0;C led to the lowest lignin residue (1.93%) and the maximum release of cellulose and hemicellulose, and the highest H2 production (26.01&#xa0;mL/g VS). H2 production at 35 and 55&#xa0;&#xb0;C was only 14.56 and 24.13&#xa0;mL/g VS, respectively. In order to further explore the potential of ultra-high temperature (65&#xa0;&#xb0;C), HS-AD was performed by gradient heating conditions (35 to 65&#xa0;&#xb0;C). However, compared to constant 65&#xa0;&#xb0;C, gradient heating conditions led to higher lignin residue (2.49%) and lower H2 production (13.53&#xa0;mL/g VS) than gradient heating conditions (47.98%). In addition, metagenomic analysis showed the cellulose/hemicellulose hydrolyzing bacteria and genes (mainly Thermoclostridium, and xynA, xynB, abfA, bglB and xynD), H2-producing bacteria and related genes (mainly Thermoclostridium, and nifD, nifH and nifK), and microbial movement and metabolic functions were enriched at 65&#xa0;&#xb0;C. However, the enrichment of two-component systems under gradient heating conditions resulted in a lack of highly-enriched ultra-high-temperature cellulose/hemicellulose hydrolyzing genera and related genes but rather enriched H2 consumption genera and genes (mainly Acetivibrio, and hyaB and hyaA) resulting in a weaker H2 production.<br><br>CONCLUSIONS: The lignin degradation process does not directly determine H2 accumulation, which was actually regulated by bacteria/genes contributing to H2 production/consumption. In addition, it is temperature that enhances the hydrolysis process of lignin rather than lignin-degrading enzymes, bacteria and genes by promoting microbial material transfer and metabolism. In terms of temperature, one of the key parameters of HS-AD for H2 production, we developed an important regulatory strategy, enriched the theoretical basis of temperature regulation for H2 production to further expanded the research horizon in this field. Video Abstract.},
}
@article {pmid39252078,
year = {2024},
author = {Vojvoda Zeljko, T and Kajan, K and Jalžić, B and Hu, A and Cukrov, N and Marguš, M and Cukrov, N and Marković, T and Sabatino, R and Di Cesare, A and Orlić, S},
title = {Genome-centric metagenomes unveiling the hidden resistome in an anchialine cave.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {67},
pmid = {39252078},
issn = {2524-6372},
support = {KK.01.2.1.02.0335//European Union through the European Regional Development Fund/ ; KK.01.1.1.01.0003//European Union through the European Regional Development Fund/ ; KK.01.2.1.02.0335//European Union through the European Regional Development Fund/ ; CN_00000033//European Union - NextGenerationEU/ ; CN_00000033//European Union - NextGenerationEU/ ; },
abstract = {BACKGROUND: Antibiotic resistance is a critical global concern, posing significant challenges to human health and medical treatments. Studying antibiotic resistance genes (ARGs) is essential not only in clinical settings but also in diverse environmental contexts. However, ARGs in unique environments such as anchialine caves, which connect both fresh and marine water, remain largely unexplored despite their intriguing ecological characteristics.<br><br>RESULTS: We present the first study that comprehensively explores the occurrence and distribution of ARGs and mobile genetic elements (MGEs) within an anchialine cave. Utilizing metagenomic sequencing we uncovered a wide array of ARGs with the bacitracin resistance gene, bacA and multidrug resistance genes, being the most dominant. The cave's microbial community and associated resistome were significantly influenced by the salinity gradient. The discovery of novel &#x3b2;-lactamase variants revealed the cave's potential as a reservoir for previously undetected resistance genes. ARGs in the cave demonstrated horizontal transfer potential via plasmids, unveiling ecological implications.<br><br>CONCLUSIONS: These findings highlight the need for further exploration of the resistome in unique environments like anchialine caves. The interconnected dynamics of ARGs and MGEs within anchialine caves offer valuable insights into potential reservoirs and mechanisms of antibiotic resistance in natural ecosystems. This study not only advances our fundamental understanding but also highlights the need for a comprehensive approach to address antibiotic resistance in diverse ecological settings.},
}
@article {pmid39252069,
year = {2024},
author = {Buddle, S and Forrest, L and Akinsuyi, N and Martin Bernal, LM and Brooks, T and Venturini, C and Miller, C and Brown, JR and Storey, N and Atkinson, L and Best, T and Roy, S and Goldsworthy, S and Castellano, S and Simmonds, P and Harvala, H and Golubchik, T and Williams, R and Breuer, J and Morfopoulou, S and Torres Montaguth, OE},
title = {Evaluating metagenomics and targeted approaches for diagnosis and surveillance of viruses.},
journal = {Genome medicine},
volume = {16},
number = {1},
pages = {111},
pmid = {39252069},
issn = {1756-994X},
mesh = {*Metagenomics/methods ; Humans ; *Viruses/genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing/methods ; Virus Diseases/diagnosis/virology ; Metagenome ; Sensitivity and Specificity ; },
abstract = {BACKGROUND: Metagenomics is a powerful approach for the detection of unknown and novel pathogens. Workflows based on Illumina short-read sequencing are becoming established in diagnostic laboratories. However, high sequencing depth requirements, long turnaround times, and limited sensitivity hinder broader adoption. We investigated whether we could overcome these limitations using protocols based on untargeted sequencing with Oxford Nanopore Technologies (ONT), which offers real-time data acquisition and analysis, or a targeted panel approach, which allows the selective sequencing of known pathogens and could improve sensitivity.<br><br>METHODS: We evaluated detection of viruses with readily available untargeted metagenomic workflows using Illumina and ONT, and an Illumina-based enrichment approach using the Twist Bioscience Comprehensive Viral Research Panel (CVRP), which targets 3153 viruses. We tested samples consisting of a dilution series of a six-virus mock community in a human DNA/RNA background, designed to resemble clinical specimens with low microbial abundance and high host content. Protocols were designed to retain the host transcriptome, since this could help confirm the absence of infectious agents. We further compared the performance of commonly used taxonomic classifiers.<br><br>RESULTS: Capture with the Twist CVRP increased sensitivity by at least 10-100-fold over untargeted sequencing, making it suitable for the detection of low viral loads (60 genome copies per ml (gc/ml)), but additional methods may be needed in a diagnostic setting to detect untargeted organisms. While untargeted ONT had good sensitivity at high viral loads (60,000 gc/ml), at lower viral loads (600-6000 gc/ml), longer and more costly sequencing runs would be required to achieve sensitivities comparable to the untargeted Illumina protocol. Untargeted ONT provided better specificity than untargeted Illumina sequencing. However, the application of robust thresholds standardized results between taxonomic classifiers. Host gene expression analysis is optimal with untargeted Illumina sequencing but possible with both the CVRP and ONT.<br><br>CONCLUSIONS: Metagenomics has the potential to become standard-of-care in diagnostics and is a powerful tool for the discovery of emerging pathogens. Untargeted Illumina and ONT metagenomics and capture with the Twist CVRP have different advantages with respect to sensitivity, specificity, turnaround time and cost, and the optimal method will depend on the clinical context.},
}
@article {pmid39251745,
year = {2024},
author = {Serwecińska, L and Font-Nájera, A and Strapagiel, D and Lach, J and Tołoczko, W and Bołdak, M and Urbaniak, M},
title = {Sewage sludge fertilization affects microbial community structure and its resistome in agricultural soils.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {21034},
pmid = {39251745},
issn = {2045-2322},
support = {No. 2020/39/B/NZ9/01772//Narodowe Centrum Nauki/ ; No. 2020/39/B/NZ9/01772//Narodowe Centrum Nauki/ ; },
mesh = {*Sewage/microbiology ; *Soil Microbiology ; *Agriculture/methods ; *Fertilizers ; *Soil/chemistry ; *Microbiota/genetics/drug effects ; Bacteria/genetics/drug effects/classification ; Metagenomics/methods ; Drug Resistance, Microbial/genetics ; Poland ; },
abstract = {Global sewage sludge production is rapidly increasing, and its safe disposal is becoming an increasingly serious issue. One of the main methods of municipal sewage sludge management is based on its agricultural use. The wastewater and sewage sludge contain numerous antibiotic resistance genes (ARGs), and its microbiome differs significantly from the soil microbial community. The aim of the study was to assess the changes occurring in the soil microbial community and resistome after the addition of sewage sludge from municipal wastewater treatment plant (WWTP) in central Poland, from which the sludge is used for fertilizing agricultural soils on a regular basis. This study used a high-throughput shotgun metagenomics approach to compare the microbial communities and ARGs present in two soils fertilized with sewage sludge. The two soils represented different land uses and different physicochemical and granulometric properties. Both soils were characterized by a similar taxonomic composition of the bacterial community, despite dissimilarities between soils properties. Five phyla predominated, viz. Planctomycetes, Actinobacteria, Proteobacteria, Chloroflexi and Firmicutes, and they were present in comparable proportions in both soils. Network analysis revealed that the application of sewage sludge resulted in substantial qualitative and quantitative changes in bacterial taxonomic profile, with most abundant phyla being considerably depleted and replaced by Proteobacteria and Spirochaetes. In addition, the ratio of oligotrophic to copiotrophic bacteria substantially decreased in both amended soils. Furthermore, fertilized soils demonstrated greater diversity and richness of ARGs compared to control soils. The increased abundance concerned mainly genes of resistance to antibiotics most commonly used in human and animal medicine. The level of heavy metals in sewage sludge was low and did not exceed the standards permitted in Poland for sludge used in agriculture, and their level in fertilized soils was still inconsiderable.},
}
@article {pmid39251728,
year = {2024},
author = {Cai, X and Dai, J and Xie, Y and Xu, S and Liu, M},
title = {Multi-omics study unravels gut microbiota and metabolites alteration in patients with Wilson's disease.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {21025},
pmid = {39251728},
issn = {2045-2322},
support = {JCYJ20220530165400002//Shenzhen Science and Technology Innovation Program/ ; 2021R01132//Shenzhen Guangming District Economic Development Special Fund/ ; },
mesh = {Humans ; *Hepatolenticular Degeneration/metabolism/microbiology/genetics ; *Gastrointestinal Microbiome ; Female ; Male ; Adult ; RNA, Ribosomal, 16S/genetics ; Metabolomics/methods ; Feces/microbiology ; Metabolome ; Young Adult ; Bacteria/classification/metabolism/genetics/isolation &amp; purification ; Metagenomics/methods ; Adolescent ; Multiomics ; },
abstract = {Hepatolenticular degeneration (HLD), also known as Wilson's disease (WD), is a rare autosomal recessive disorder regarding copper metabolism. Whether gut microbiota imbalance is involved in developing HLD remains unknown. A comprehensive 16S rRNA amplicon sequencing, metagenomic sequencing, and metabonomic analysis were undertaken in patients with WD to analyze the composition and function profiles of gut microbiota in patients with WD. The data demonstrated differences in gut microbiota and metabolic pathways between WD patients and normal individuals, significantly decreasing bacterial richness and diversity. The levels of Selenomonaceae and Megamonas in WD patients are significantly higher than those in healthy individuals. The relative abundances of Roseburia inulinivorans in patients with WD are lower than in healthy individuals. Compared with healthy people, the level of metabolites in patients with WD is abnormal. Leucylproline, 5-Phenylvaleric Acid and N-Desmethylclobazam, which have nutritional and protective effects, are significantly reduced fecal metabolites in patients with WD. D-Gluconic acid, which can chelate metal ions, may be a potential treatment for WD. The positive correlation it demonstrates with Alistipes indistinctus and Prevotella stercora indicates potential bacteria able to treat WD. These metabolites are mainly related to the biosynthesis of antibiotics, alpha-linolenic acid metabolism, one carbon pool by folate, nicotinate and nicotinamide metabolism. In conclusion, the data from this study elucidate novel mechanisms describing how abnormal gut miccrobiota contribute to the pathogenesis of WD and outlines new molecules for the treatment of WD.},
}
@article {pmid39250478,
year = {2024},
author = {Pusa, T and Rousu, J},
title = {Stable biomarker discovery in multi-omics data via canonical correlation analysis.},
journal = {PloS one},
volume = {19},
number = {9},
pages = {e0309921},
pmid = {39250478},
issn = {1932-6203},
mesh = {Humans ; *Biomarkers/metabolism ; *Inflammatory Bowel Diseases/metabolism ; *Metabolomics/methods ; Metagenomics/methods ; Machine Learning ; Gastrointestinal Microbiome ; Multiomics ; },
abstract = {Multi-omics analysis offers a promising avenue to a better understanding of complex biological phenomena. In particular, untangling the pathophysiology of multifactorial health conditions such as the inflammatory bowel disease (IBD) could benefit from simultaneous consideration of several omics levels. However, taking full advantage of multi-omics data requires the adoption of suitable new tools. Multi-view learning, a machine learning technique that natively joins together heterogeneous data, is a natural source for such methods. Here we present a new approach to variable selection in unsupervised multi-view learning by applying stability selection to canonical correlation analysis (CCA). We apply our method, StabilityCCA, to simulated and real multi-omics data, and demonstrate its ability to find relevant variables and improve the stability of variable selection. In a case study on an IBD microbiome data set, we link together metagenomics and metabolomics, revealing a connection between their joint structure and the disease, and identifying potential biomarkers. Our results showcase the usefulness of multi-view learning in multi-omics analysis and demonstrate StabilityCCA as a powerful tool for biomarker discovery.},
}
@article {pmid39250184,
year = {2024},
author = {Pallen, MJ},
title = {The dynamic history of prokaryotic phyla: discovery, diversity and division.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {74},
number = {9},
pages = {},
pmid = {39250184},
issn = {1466-5034},
mesh = {*Bacteria/genetics/classification ; *Phylogeny ; Archaea/genetics/classification ; History, 20th Century ; History, 21st Century ; Prokaryotic Cells/classification ; Classification/methods ; },
abstract = {Here, I review the dynamic history of prokaryotic phyla. Following leads set by Darwin, Haeckel and Woese, the concept of phylum has evolved from a group sharing common phenotypes to a set of organisms sharing a common ancestry, with modern taxonomy based on phylogenetic classifications drawn from macromolecular sequences. Phyla came as surprising latecomers to the formalities of prokaryotic nomenclature in 2021. Since then names have been validly published for 46 prokaryotic phyla, replacing some established names with neologisms, prompting criticism and debate within the scientific community. Molecular barcoding enabled phylogenetic analysis of microbial ecosystems without cultivation, leading to the identification of candidate divisions (or phyla) from diverse environments. The introduction of metagenome-assembled genomes marked a significant advance in identifying and classifying uncultured microbial phyla. The lumper-splitter dichotomy has led to disagreements, with experts cautioning against the pressure to create a profusion of new phyla and prominent databases adopting a conservative stance. The Candidatus designation has been widely used to provide provisional status to uncultured prokaryotic taxa, with phyla named under this convention now clearly surpassing those with validly published names. The Genome Taxonomy Database (GTDB) has offered a stable, standardized prokaryotic taxonomy with normalized taxonomic ranks, which has led to both lumping and splitting of pre-existing phyla. The GTDB framework introduced unwieldy alphanumeric placeholder labels, prompting recent publication of over 100 user-friendly Latinate names for unnamed prokaryotic phyla. Most candidate phyla remain 'known unknowns', with limited knowledge of their genomic diversity, ecological roles, or environments. Whether phyla still reflect significant evolutionary and ecological partitions across prokaryotic life remains an area of active debate. However, phyla remain of practical importance for microbiome analyses, particularly in clinical research. Despite potential diminishing returns in discovery of biodiversity, prokaryotic phyla offer extensive research opportunities for microbiologists for the foreseeable future.},
}
@article {pmid39248562,
year = {2024},
author = {Xiao, JZ and Nesbø, CL and Molenda, O and Toth, CRA and Edwards, EA},
title = {Metagenomic and genomic sequences from a nitrate-reducing benzene-degrading enrichment culture.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0029424},
doi = {10.1128/mra.00294-24},
pmid = {39248562},
issn = {2576-098X},
abstract = {Metagenome-assembled genomes (MAGs) were recovered from metagenomic assemblies from a nitrate-reducing benzene-degrading enrichment culture. Ten MAGs of high quality or functional interest to benzene degradation are reported, seven of which are single contig genomes.},
}
@article {pmid39248477,
year = {2024},
author = {Hu, N-n and Wang, Z-q and Zhang, S-j and Wang, Z-z and Chen, X-x},
title = {Characterization of larval gut microbiota of two endoparasitoid wasps associated with their common host, Plutella xylostella (Linnaeus) (Lepidoptera: Plutellidae).},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0120824},
doi = {10.1128/spectrum.01208-24},
pmid = {39248477},
issn = {2165-0497},
abstract = {Insect gut microbes play important roles in digestion, metabolism, development, and environmental adaptation. Parasitoid wasps are one of the most important biological control agents in pest control, while the gut microbial species compositions and the associated functions have been poorly investigated. Two endoparasitoid wasps, Cotesia vestalis and Diadromus collaris, parasitize the larval stage and pupal stage of the diamondback moth, Plutella xylostella, respectively. Using whole-genome shotgun metagenomic sequencing, we characterized the gut microbial composition, diversity, and potential functional roles associated with the two parasitoid wasp larvae. The results reveal that Proteobacteria and Firmicutes are the dominant phyla in the gut of C. vestalis and D. collaris larvae, with Rhizobium and Enterococcus being the dominant genera. The putative microbial functions associated with the two parasitoid wasps might play a virtual role in assisting in consuming the host's nutritional composition. The enriched CAZymes family genes are primarily involved in the degradation and synthesis of chitin. Despite the richness of microbial species and communities, the microbes species and the microbial community structure exhibit significant similarity between the two parasitoid wasps and between the parasitoid wasp and the host P. xylostella. Notably, the prevalence of the genus Enterococcus shared among them suggests a possible link of gut microbes between the host and their associated parasitoids. Our study offers insights into the gut microbe-based interactions between the host and parasitoid wasps for the first time, potentially paving the way for the development of an ecologically friendly biocontrol strategy against the pest P. xylostella.IMPORTANCEEndoparasitoid wasps spend the majority of their lifespan within their host and heavily rely on the host's nutrition for survival. There is limited understanding regarding the composition and physiological impacts of gut microbial communities in parasitoid wasps, particularly during the larval stage, which is directly linked to the host. Based on a thorough characterization of the gut microbe and comprehensive comparative analysis, we found the microbial species of the larval parasitoid wasp Cotesia vestalis and the pupal parasitoid wasp Diadromus collaris were similar, sharing 159 genera and 277 species, as were the microbial community structure. Certain of the dominant microbial strains of the two parasitoid wasps were similar to that of their host Plutella xylostella larvae, revealing host insect may affect the microbial community of the parasitoid wasps. The putative microbial functions associated with the parasitoid wasp larvae play an important role in dietary consumption.},
}
@article {pmid39248463,
year = {2024},
author = {Zhang, X and Wu, N and Geng, K and Yuan, C and Wang, B and Shi, J and Qiu, J and He, J},
title = {Identification of a chlorosalicylic acid decarboxylase (CsaD) involved in decarboxylation of 3,6-DCSA from an anaerobic dicamba-degrading sludge.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0131924},
doi = {10.1128/aem.01319-24},
pmid = {39248463},
issn = {1098-5336},
abstract = {3,6-Dichlorosalicylic acid (3,6-DCSA) is the demethylation metabolite of herbicide 3,6-dichloro-2-methoxy benzoic acid (dicamba). Previous studies have shown that anaerobic sludge further transformed 3,6-DCSA through decarboxylation and dechlorination. However, the anaerobe, enzyme, and gene involved in the anaerobic degradation of 3,6-DCSA are still unknown. In this study, an anaerobic sludge that efficiently degraded dicamba was enriched, and a 3,6-DCSA decarboxylase, designated chlorosalicylic acid decarboxylase (CsaD), was partially purified and identified from the anaerobic sludge. Metagenomic analysis showed that the csaD gene was located in a gene cluster of metagenome-assembled genome 8 (MAG8). MAG8 belonged to an uncultured order, OPB41, in the class Coriobacteriia of the phylum Actinobacteria, and its abundance increased approximately once during the enrichment process. CsaD was a non-oxidative decarboxylase in the amidohydrolase 2 family catalyzing the decarboxylation of 3,6-DCSA and 6-chlorosalicylic acid (6-CSA). Its affinity and catalytic efficiency for 3,6-DCSA were significantly higher than those for 6-CSA. This study provides new insights into the anaerobic catabolism of herbicide dicamba.IMPORTANCEDicamba, an important hormone herbicide, easily migrates to anoxic habitats such as sediment, ground water, and deep soil. Thus, the anaerobic catabolism of dicamba is of importance. Anaerobic bacteria or sludge demethylated dicamba to 3,6-DCSA, and in a previous study, based on metabolite identification, it was proposed that 3,6-DCSA be further degraded via two pathways: decarboxylation to 2,5-dichlorophenol, then dechlorination to 3-chlorophenol (3-CP); or dechlorination to 6-CSA, then decarboxylation to 3-CP. However, there was no physiological and genetic validation for the pathway. In this study, CsaD catalyzed the decarboxylation of both 3,6-DCSA and 6-CSA, providing enzyme-level evidence for the anaerobic catabolism of 3,6-DCSA through the two pathways. CsaD was located in MAG8, which belonged to an uncultured anaerobic actinomycetes order, OPB41, indicating that anaerobic actinomycetes in OPB41 was involved in the decarboxylation of 3,6-DCSA. This study provides a basis for understanding the anaerobic catabolism of dicamba and the demethylation product, 3,6-DCSA.},
}
@article {pmid39248279,
year = {2024},
author = {Ohuchi, H and Asano, R and Mori, A and Ishibashi, T and Motooka, D and Nakai, M and Nakaoka, Y},
title = {Gut Dysbiosis in Patients With Fontan Circulation.},
journal = {Journal of the American Heart Association},
volume = {13},
number = {18},
pages = {e034538},
doi = {10.1161/JAHA.124.034538},
pmid = {39248279},
issn = {2047-9980},
mesh = {Humans ; Male ; *Dysbiosis ; *Fontan Procedure/adverse effects ; Female ; *Gastrointestinal Microbiome/physiology ; Adolescent ; Child ; Heart Defects, Congenital/surgery ; Case-Control Studies ; Young Adult ; Feces/microbiology ; Hemodynamics ; Biomarkers/blood/metabolism ; Adult ; },
abstract = {BACKGROUND: The process underlying Fontan pathophysiology is multifactorial and may include gut dysbiosis (GD). We investigated the presence of GD and elucidated its correlation with Fontan pathophysiology.<br><br>METHODS AND RESULTS: Gut microbiomes of 155 consecutive patients with Fontan pathophysiology and 44 healthy individuals were analyzed using 16S rRNA sequencing of bacterial DNA extracted from fecal samples. GD was evaluated on the basis of &#x3b1; and &#xdf; diversities of the gut microbiome and was compared with natural log-transformed C-reactive protein, hemodynamics, von Willebrand factor antigen (a bacterial translocation marker), Mac-2 binding protein glycosylation isomer (a liver fibrosis indicator), peak oxygen uptake, and heart failure hospitalization. Patients with Fontan exhibited GD in terms of &#x3b1; and &#xdf; diversities as compared with controls (P<0.01). Reduced &#x3b1; diversity was associated with a failed hemodynamic phenotype, hypoxia, high natural log-transformed C-reactive protein levels, and elevated von Willebrand factor antigen and Mac-2 binding protein glycosylation isomer levels (P<0.05-0.01). In addition to elevated von Willebrand factor antigen and hypoxia, decreased &#x3b1; diversity was independently correlated with a high natural log-transformed C-reactive protein level (P<0.05), which was associated with liver imaging abnormalities and a heightened risk of heart failure hospitalization (P<0.01 for both).<br><br>CONCLUSIONS: Patients with Fontan pathophysiology exhibited GD compared with healthy individuals, and GD was linked to failed hemodynamics and systemic inflammation with a poor prognosis. Therefore, GD may play a pivotal role in a failing Fontan status, including Fontan-associated liver disease, through GD-associated systemic inflammation.},
}
@article {pmid39248272,
year = {2024},
author = {Chen, X and He, Y and Zhou, L and Li, X and Jiang, M and Wu, M and Li, J and Chen, L and Xu, H and Gui, L and Zhou, Z},
title = {Microbial Heterogeneity Identification of Cerebral Thrombi Via Metagenomic Next-Generation Sequencing-Based Strategy.},
journal = {Journal of the American Heart Association},
volume = {13},
number = {18},
pages = {e033221},
doi = {10.1161/JAHA.123.033221},
pmid = {39248272},
issn = {2047-9980},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing ; *Metagenomics/methods ; Female ; Male ; Middle Aged ; *Intracranial Thrombosis/microbiology/genetics ; Aged ; Ischemic Stroke/microbiology/genetics ; Bacteria/genetics/isolation &amp; purification ; Microbiota/genetics ; },
abstract = {BACKGROUND: Diagnosis of the cause of cerebral thrombi is vital for recurrence prevention but also challenging. The presence of the microbiome has recently been confirmed in thrombus, suggesting a novel approach to distinguish cerebral thrombi of different origins. However, little is known about whether there is heterogeneity in microbiological colonization of cerebral thrombi of different sources.<br><br>METHODS AND RESULTS: Forty patients experiencing acute ischemic stroke were included and clinical data were collected. Metagenomic next-generation sequencing was adopted to detect bacterial and genomic signatures of human cerebral thrombi samples. We found similar species diversity between the large-artery atherosclerosis thrombi and cardioembolic thrombi but different species composition and distribution of cerebral thrombus microbiota. Compared with the group with cardioembolism, the group with large-artery atherosclerosis showed a significantly higher relative abundance of Ralstonia insidiosa among the top 10 bacterial species in cerebral thrombi. Twenty operational taxonomy units were correlated with 11 clinical indicators of ischemic stroke. The Gene Ontology enrichment analysis revealed 9 different enriched biological processes (translation and carbohydrate metabolic process, etc). The enriched Kyoto Encyclopedia of Genes and Genomes pathways included ribosome, butanoate metabolism, and sulfur metabolism.<br><br>CONCLUSIONS: This study, based on the approach of metagenomic next-generation sequencing, provides a diagnostic microbiological method to discriminate individuals with cardioembolic thrombi from those with large-artery atherosclerosis thrombi with human cerebral thrombi samples. Our findings provide a fresh perspective on microbial heterogeneity of cerebral thrombi and demonstrate biological processes and pathway features of cerebral thrombi.},
}
@article {pmid39247916,
year = {2024},
author = {Lyu, X and Xu, X and Shen, S and Qin, F},
title = {Genetics causal analysis of oral microbiome on type 2 diabetes in East Asian populations: a bidirectional two-sample Mendelian randomized study.},
journal = {Frontiers in endocrinology},
volume = {15},
number = {},
pages = {1452999},
pmid = {39247916},
issn = {1664-2392},
mesh = {Humans ; *Diabetes Mellitus, Type 2/microbiology/genetics ; East Asian People/genetics ; Genetic Predisposition to Disease ; *Genome-Wide Association Study ; *Mendelian Randomization Analysis ; *Microbiota/genetics ; Mouth/microbiology ; *Saliva/microbiology ; Tongue/microbiology ; },
abstract = {INTRODUCTION: The dysbiosis of the oral microbiome is associated with the progression of various systemic diseases, including diabetes. However, the precise causal relationships remain elusive. This study aims to investigate the potential causal associations between oral microbiome and type 2 diabetes (T2D) using Mendelian randomization (MR) analyses.<br><br>METHODS: We conducted bidirectional two-sample MR analyses to investigate the impact of oral microbiome from saliva and the tongue T2D. This analysis was based on metagenome-genome-wide association studies (mgGWAS) summary statistics of the oral microbiome and a large meta-analysis of GWAS of T2D in East Asian populations. Additionally, we utilized the T2D GWAS summary statistics from the Biobank Japan (BBJ) project for replication. The MR methods employed included Wald ratio, inverse variance weighting (IVW), weighted median, MR-Egger, contamination mixture (ConMix), and robust adjusted profile score (RAPS).<br><br>RESULTS: Our MR analyses revealed genetic associations between specific bacterial species in the oral microbiome of saliva and tongue with T2D in East Asian populations. The MR results indicated that nine genera were shared by both saliva and tongue. Among these, the genera Aggregatibacter, Pauljensenia, and Prevotella were identified as risk factors for T2D. Conversely, the genera Granulicatella and Haemophilus D were found to be protective elements against T2D. However, different species within the genera Catonella, Lachnoanaerobaculum, Streptococcus, and Saccharimonadaceae TM7x exhibited multifaceted influences; some species were positively correlated with the risk of developing T2D, while others were negatively correlated.<br><br>DISCUSSION: This study utilized genetic variation tools to confirm the causal effect of specific oral microbiomes on T2D in East Asian populations. These findings provide valuable insights for the treatment and early screening of T2D, potentially informing more targeted and effective therapeutic strategies.},
}
@article {pmid39247756,
year = {2024},
author = {Lu, Y and Zhang, D and Han, D and Yu, F and Ye, X and Zheng, S},
title = {Case Report: Diagnosis of Hemolytic Anemia from Babesia and Secondary Multi-Pathogen Pneumonia Using a Metagenomic Next-Generation Sequencing Approach.},
journal = {Infection and drug resistance},
volume = {17},
number = {},
pages = {3785-3791},
pmid = {39247756},
issn = {1178-6973},
abstract = {Babesiosis, as a vector-borne infectious disease, remains relatively rare and is prone to being overlooked and misdiagnosed. Therefore, understanding the epidemiological characteristics and clinical manifestations of babesiosis is crucial for the prompt detection and treatment of the disease. We reported a 63-year-old male patient presenting with spontaneous fever and chills. Laboratory investigations revealed erythrocytopenia, reduced hemoglobin levels, and increased reticulocytes and total bilirubin. Bone marrow examination indicated vigorous cell proliferation, a decreased granulocyte to red cell ratio, and predominant erythroid cell proliferation, with a higher prevalence of intermediate and late-stage juvenile granulocyte and erythroid cells. Initial treatment focused on hemophagocytic syndrome triggered by Epstein-Barr virus infection yielded unsatisfactory results, leading to secondary multiple pulmonary infections. Metagenomic next-generation sequencing (mNGS) of sputum samples pointed to hemolytic anemia induced by Babesia infection, which was subsequently confirmed through peripheral blood smear analysis. The patient responded well to prompt administration of atovaquone and azithromycin, with symptoms resolving and laboratory parameters normalizing. Hemolytic anemia resulting from babesiosis should be distinguished from hemophagocytic syndrome caused by Epstein-Barr virus and other hematologic conditions. mNGS represents an efficient technique for Babesia detection.},
}
@article {pmid39247454,
year = {2024},
author = {Rajguru, B and Shri, M and Bhatt, VD},
title = {Exploring microbial diversity in the rhizosphere: a comprehensive review of metagenomic approaches and their applications.},
journal = {3 Biotech},
volume = {14},
number = {10},
pages = {224},
pmid = {39247454},
issn = {2190-572X},
abstract = {The rhizosphere, the soil region influenced by plant roots, represents a dynamic microenvironment where intricate interactions between plants and microorganisms shape soil health, nutrient cycling, and plant growth. Soil microorganisms are integral players in the transformation of materials, the dynamics of energy flows, and the intricate cycles of biogeochemistry. Considerable research has been dedicated to investigating the abundance, diversity, and intricacies of interactions among different microbes, as well as the relationships between plants and microbes present in the rhizosphere. Metagenomics, a powerful suite of techniques, has emerged as a transformative tool for dissecting the genetic repertoire of complex microbial communities inhabiting the rhizosphere. The review systematically navigates through various metagenomic approaches, ranging from shotgun metagenomics, enabling unbiased analysis of entire microbial genomes, to targeted sequencing of the 16S rRNA gene for taxonomic profiling. Each approach's strengths and limitations are critically evaluated, providing researchers with a nuanced understanding of their applicability in different research contexts. A central focus of the review lies in the practical applications of rhizosphere metagenomics in various fields including agriculture. By decoding the genomic content of rhizospheric microbes, researchers gain insights into their functional roles in nutrient acquisition, disease suppression, and overall plant health. The review also addresses the broader implications of metagenomic studies in advancing our understanding of microbial diversity and community dynamics in the rhizosphere. It serves as a comprehensive guide for researchers, agronomists, and policymakers, offering a roadmap for harnessing metagenomic approaches to unlock the full potential of the rhizosphere microbiome in promoting sustainable agriculture.},
}
@article {pmid39246231,
year = {2024},
author = {Du, Y and Zuo, W and Sun, F},
title = {Imputing Metagenomic Hi-C Contacts Facilitates the Integrative Contig Binning Through Constrained Random Walk with Restart.},
journal = {Journal of computational biology : a journal of computational molecular cell biology},
volume = {},
number = {},
pages = {},
doi = {10.1089/cmb.2024.0663},
pmid = {39246231},
issn = {1557-8666},
abstract = {Metagenomic Hi-C (metaHi-C) has shown remarkable potential for retrieving high-quality metagenome-assembled genomes from complex microbial communities. Nevertheless, existing metaHi-C-based contig binning methods solely rely on Hi-C interactions between contigs, disregarding crucial biological information such as the presence of single-copy marker genes. To overcome this limitation, we introduce ImputeCC, an integrative contig binning tool optimized for metaHi-C datasets. ImputeCC integrates both Hi-C interactions and the discriminative power of single-copy marker genes to group marker-gene-containing contigs into preliminary bins. It also introduces a novel constrained random walk with restart algorithm to enhance Hi-C connectivity among contigs. Comprehensive assessments using both mock and real metaHi-C datasets from diverse environments demonstrate that ImputeCC consistently outperforms other Hi-C-based contig binning tools. A genus-level analysis of the sheep gut microbiota reconstructed by ImputeCC underlines its capability to recover key species from dominant genera and identify previously unknown genera.},
}
@article {pmid39245657,
year = {2024},
author = {Lee, S and Meslier, V and Bidkhori, G and Garcia-Guevara, F and Etienne-Mesmin, L and Clasen, F and Park, J and Plaza Oñate, F and Cai, H and Le Chatelier, E and Pons, N and Pereira, M and Seifert, M and Boulund, F and Engstrand, L and Lee, D and Proctor, G and Mardinoglu, A and Blanquet-Diot, S and Moyes, D and Almeida, M and Ehrlich, SD and Uhlen, M and Shoaie, S},
title = {Transient colonizing microbes promote gut dysbiosis and functional impairment.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {80},
pmid = {39245657},
issn = {2055-5008},
support = {EP/S001301/1//RCUK | Engineering and Physical Sciences Research Council (EPSRC)/ ; BB/S016899/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; N/A//Science for Life Laboratory (SciLifeLab)/ ; },
mesh = {*Dysbiosis/microbiology ; *Gastrointestinal Microbiome ; Humans ; *Metagenomics/methods ; Sweden ; *Bacteria/classification/genetics/isolation &amp; purification ; *Feces/microbiology ; Longitudinal Studies ; Metagenome ; Adult ; Bioreactors/microbiology ; Fermentation ; },
abstract = {Species composition of the healthy adult gut microbiota tends to be stable over time. Destabilization of the gut microbiome under the influence of different factors is the main driver of the microbial dysbiosis and subsequent impacts on host physiology. Here, we used metagenomics data from a Swedish longitudinal cohort, to determine the stability of the gut microbiome and uncovered two distinct microbial species groups; persistent colonizing species (PCS) and transient colonizing species (TCS). We validated the continuation of this grouping, generating gut metagenomics data for additional time points from the same Swedish cohort. We evaluated the existence of PCS/TCS across different geographical regions and observed they are globally conserved features. To characterize PCS/TCS phenotypes, we performed bioreactor fermentation with faecal samples and metabolic modeling. Finally, using chronic disease gut metagenome and other multi-omics data, we identified roles of TCS in microbial dysbiosis and link with abnormal changes to host physiology.},
}
@article {pmid39245322,
year = {2024},
author = {Jiménez, JD and Godoy, MS and Del Cerro, C and Prieto, MA},
title = {Hints from nature for a PHA circular economy: Carbon synthesis and sharing by Pseudomonas solani GK13.},
journal = {New biotechnology},
volume = {84},
number = {},
pages = {9-23},
doi = {10.1016/j.nbt.2024.09.002},
pmid = {39245322},
issn = {1876-4347},
abstract = {Polyhydroxyalkanoates (PHAs) are a well-known group of biodegradable and biocompatible bioplastics that are synthesised and stored by microorganisms as carbon and energy reservoirs. Extracellular PHA depolymerases (ePhaZs), secreted by a limited range of microorganisms, are the main hydrolytic enzymes responsible for their environmental degradation. Pseudomonas sp. GK13, initially identified as P. fluorescens GK13, produces PHA and a prototypic ePhaZ that specifically degrades mcl-PHA. In this study, a comprehensive characterization of strain GK13 was performed. The whole genomic sequence of GK13 was consolidated into one complete chromosome, leading to its reclassification as P. solani GK13. We conducted a detailed in silico examination of the bacteria genomic sequence, specifically targeting PHA metabolic functions. From the different growth conditions explored, PHA accumulation occurred only under carbon/nitrogen (C/N) imbalance, whereas ePhaZ production was induced even at balanced C/N ratios in mineral media. We extend our study to other bacteria belonging to the Pseudomonas genus revealing that the ePhaZ production capacity is closely associated with mcl-PHA synthesis capacity, as also suggested by metagenomic samples. This finding suggests that these types of microorganisms could contribute to the carbon economy of the microbial community, by storing PHA in carbon-rich times, and sharing it with the rest of the population during times of carbon scarcity through PHA hydrolysis. The conclusion pointed that carbon cycle metabolism performed by P. solani GK13 may contribute to the environmental circular economy at a microscopic scale.},
}
@article {pmid39245190,
year = {2024},
author = {Huang, J and Liu, S and Li, P and Wei, L and Lin, G and Lin, J and Luo, Y and Liu, Y and Mao, Y and Ruan, H and Qin, B and Fan, P and Lu, T and Cai, W and Yi, H and Mou, X and Lu, Z and Zhao, W and Wu, A},
title = {Multi-omics analysis of gut-brain axis reveals novel microbial and neurotransmitter signatures in patients with arteriosclerotic cerebral small vessel disease.},
journal = {Pharmacological research},
volume = {208},
number = {},
pages = {107385},
doi = {10.1016/j.phrs.2024.107385},
pmid = {39245190},
issn = {1096-1186},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Cerebral Small Vessel Diseases/metabolism/microbiology ; Male ; *Brain-Gut Axis ; Female ; Aged ; Middle Aged ; *Neurotransmitter Agents/metabolism ; *Dysbiosis/microbiology ; Metabolomics ; Bacteria/metabolism/genetics ; Metabolome ; Multiomics ; },
abstract = {Arteriosclerotic cerebral small vessel disease (aCSVD) is a major cause of stroke and dementia. Although its underlying pathogenesis remains poorly understood, both inflammaging and gut microbiota dysbiosis have been hypothesized to play significant roles. This study investigated the role of gut microbiota in the pathogenesis of aCSVD through a comparative analysis of the gut microbiome and metabolome between CSVD patients and healthy controls. The results showed that patients with aCSVD exhibited a marked reduction in potentially beneficial bacterial species, such as Faecalibacterium prausnitzli and Roseburia intestinalis, alongside an increase in taxa from Bacteroides and Proteobacteria. Integrated metagenomic and metabolomic analyses revealed that alterations in microbial metabolic pathways, including LPS biosynthesis and phenylalanine-tyrosine metabolism, were associated with the status of aCSVD. Our findings indicated that microbial LPS biosynthesis and phenylalanine-tyrosine metabolism potentially influenced the symptoms and progression of aCSVD via pro-inflammatory effect and modulation of systemic neurotransmitters, respectively. These results imply that gut microbiota characteristics may serve as indicators for early detection of aCSVD and as potential gut-directed therapeutic intervention target.},
}
@article {pmid39245157,
year = {2024},
author = {Zhang, L and Xu, W and Zhao, Y and Sui, L and Song, M and Liu, Q},
title = {Identification and characterization of Jingmen tick virus from Rhipicephalus microplus in Hunan, China.},
journal = {Acta tropica},
volume = {260},
number = {},
pages = {107378},
doi = {10.1016/j.actatropica.2024.107378},
pmid = {39245157},
issn = {1873-6254},
abstract = {Jingmen tick virus (JMTV) is a tick-borne pathogen known to affect human beings, characterized by a segmented genome structure that defies the conventional understanding of the Flaviviridae family. In the present study, we employed metagenomic analysis to screen for tick-borne viruses in Hunan Province, China, and identified five JMTV variants with complete genomes from Rhipicephalus microplus ticks sampled from cattle. These viral strains exhibited the highest sequence similarity to JMTV isolates previously reported in Hubei Province, China. However, evidence of genomic reassortment was detected, particularly with the S2 segment showing greater similarity to the strains from Japan. Phylogenetic analysis demonstrated that JMTV strains cluster predominantly based on their geographic origin. In agreement with the homology data, the S1, S3, and S4 segments of the strains identified in this study grouped with those from Hubei Province, while the S2 segment displayed a distinct topological structure. Moreover, JMTV displayed limited replication in mammal-derived cells, but thrived in tick-derived cell lines. In addition to the commonly used R. microplus-derived BME/CTVM23 cells, we found that JMTV also proliferated robustly in both Ixodes scapularis-derived ISE6 and Ixodes ricinus-derived IRE/CTVM19 cells, offering new avenues for in vitro production of the virus. In summary, this study expands the known geographic distribution and genetic diversity of JMTV, providing valuable insights into its epidemiology and potential for in vitro cultivation.},
}
@article {pmid39244980,
year = {2024},
author = {Zhao, S and Zhang, Q and Huang, Q and Zhang, C and Li, H and Siddique, KHM},
title = {Polyvinyl chloride microplastics disseminate antibiotic resistance genes in Chinese soil: A metagenomic analysis.},
journal = {Journal of hazardous materials},
volume = {479},
number = {},
pages = {135727},
doi = {10.1016/j.jhazmat.2024.135727},
pmid = {39244980},
issn = {1873-3336},
mesh = {*Polyvinyl Chloride ; *Microplastics/toxicity ; *Soil Microbiology ; China ; *Soil Pollutants/toxicity ; *Drug Resistance, Microbial/genetics ; *Bacteria/genetics/drug effects ; *Genes, Bacterial ; Metagenomics ; Drug Resistance, Bacterial/genetics ; },
abstract = {The widespread prevalence of microplastics (MPs) in the environment poses concerns as they are vectors of antibiotic resistance genes (ARGs). The relationships between antibiotic resistomes and MPs remain unexplored in soil which was considered as the reservoirs of MPs and ARGs. This study investigated the effects of polyvinyl chloride (PVC) MPs on soil bacterial communities and ARG abundance which soil samples sourced from 20 provinces across China. We found that PVC significantly influences soil bacterial community structure and ARG abundance. Structural equation modeling revealed that PVC alters soil characteristics, ultimately affecting soil bacterial communities, including ARG-containing bacterial hosts, and the relative abundance of ARGs. This study enhances our understanding of how MPs influence the proliferation and hosts of ARGs within diverse soil environments, offering crucial insights for future strategies in plastic management and disposal.},
}
@article {pmid39244926,
year = {2024},
author = {Zhang, C and Hu, J and Wang, H and Cheng, H and Cao, X and Sakamaki, T and Li, X},
title = {Sulfamethoxazole degradation in tri-electrode microbial electrochemical systems: Metabolomic and Metagenomic insights into organic pollution effects.},
journal = {Journal of environmental management},
volume = {370},
number = {},
pages = {122410},
doi = {10.1016/j.jenvman.2024.122410},
pmid = {39244926},
issn = {1095-8630},
abstract = {Organic pollutants can alter the physicochemical properties and microbial communities of water bodies. In water contaminated with organic pollutants, the unique extracellular electron transfer mechanisms that promote sulfamethoxazole (SMX) degradation in tri-electrode microbial electrochemical systems (TE-MES) may be impacted. To simulate biodegradable organic matter contamination, glucose (GLU) was added. Metagenomics and metabolomics were used to analyze changes in microbial community structure, metabolism, and function on the electrodes. GLU addition accelerated water quality deterioration, and enhanced SMX degradation. Microbial taxa on the electrodes experienced selective enrichment. Notably, methanogens and SMX-degrading bacteria were enriched, while denitrifying bacteria and antibiotic-resistant bacteria were suppressed. Enriched metabolites were linked to 15 metabolic pathways and other functions like microbial signaling and genetics. Non-redundant genes also clustered in metabolic pathways, aligning with metabolite enrichment results. Additional pathways involved life cycle processes and protein interactions. Enzymes related to carbon metabolism, particularly glycoside hydrolases, increased significantly, indicating a shift in carbon metabolism on microbial electrodes after GLU addition. The abundance of intracellular electron transfer enzymes rose, while outer membrane proteins decreased. This contrasts with the typical TE-MES mechanism where outer membrane proteins facilitate SMX degradation. The presence of organic pollution may shift SMX degradation from an extracellular electrochemical process to an intracellular metabolic process, possibly involving co-metabolism with simple organic compounds. This study provides mechanistic insights and theoretical guidance for using TE-MES with embedded microbial electrodes to treat antibiotic-contaminated water affected by organic pollution.},
}
@article {pmid39244633,
year = {2024},
author = {Li, F and Liu, J and Maldonado-Gómez, MX and Frese, SA and Gänzle, MG and Walter, J},
title = {Highly accurate and sensitive absolute quantification of bacterial strains in human fecal samples.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {168},
pmid = {39244633},
issn = {2049-2618},
mesh = {Humans ; *Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; *Limosilactobacillus reuteri/genetics/classification ; Reproducibility of Results ; DNA, Bacterial/genetics ; Real-Time Polymerase Chain Reaction/methods ; High-Throughput Nucleotide Sequencing/methods ; Limit of Detection ; Sensitivity and Specificity ; Bacteria/genetics/classification/isolation &amp; purification ; },
abstract = {BACKGROUND: Next-generation sequencing (NGS) approaches have revolutionized gut microbiome research and can provide strain-level resolution, but these techniques have limitations in that they are only semi-quantitative, suffer from high detection limits, and generate data that is compositional. The present study aimed to systematically compare quantitative PCR (qPCR) and droplet digital PCR (ddPCR) for the absolute quantification of Limosilactobacillus reuteri strains in human fecal samples and to develop an optimized protocol for the absolute quantification of bacterial strains in fecal samples.<br><br>RESULTS: Using strain-specific PCR primers for L. reuteri 17938, ddPCR showed slightly better reproducibility, but qPCR was almost as reproducible and showed comparable sensitivity (limit of detection [LOD] around 10[4] cells/g feces) and linearity (R[2]&#x2009;>&#x2009;0.98) when kit-based DNA isolation methods were used. qPCR further had a wider dynamic range and is cheaper and faster. Based on these findings, we conclude that qPCR has advantages over ddPCR for the absolute quantification of bacterial strains in fecal samples. We provide an optimized and easy-to-follow step-by-step protocol for the design of strain-specific qPCR assays, starting from primer design from genome sequences to the calibration of the PCR system. Validation of this protocol to design PCR assays for two L. reuteri strains, PB-W1 and DSM 20016[&#xa0;T], resulted in a highly accurate qPCR with a detection limit in spiked fecal samples of around 10[3] cells/g feces. Applying our strain-specific qPCR assays to fecal samples collected from human subjects who received live L. reuteri PB-W1 or DSM 20016[&#xa0;T] during a human trial demonstrated a highly accurate quantification and sensitive detection of these two strains, with a&#xa0;much lower LOD&#xa0;and a broader dynamic range compared to NGS approaches (16S rRNA gene sequencing and whole metagenome sequencing).<br><br>CONCLUSIONS: Based on our analyses, we consider qPCR with kit-based DNA extraction approaches the best approach to accurately quantify gut bacteria at the strain level in fecal samples. The provided step-by-step protocol will allow scientists to design highly sensitive strain-specific PCR systems for the accurate quantification of bacterial strains of not only L. reuteri but also other bacterial taxa in a broad range of applications and sample types. Video Abstract.},
}
@article {pmid39244624,
year = {2024},
author = {Yang, X and Feng, K and Wang, S and Yuan, MM and Peng, X and He, Q and Wang, D and Shen, W and Zhao, B and Du, X and Wang, Y and Wang, L and Cao, D and Liu, W and Wang, J and Deng, Y},
title = {Unveiling the deterministic dynamics of microbial meta-metabolism: a multi-omics investigation of anaerobic biodegradation.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {166},
pmid = {39244624},
issn = {2049-2618},
support = {No. 2019YFC1905001//National Key Research and Development Program of China/ ; },
mesh = {Anaerobiosis ; *Biodegradation, Environmental ; *Bioreactors/microbiology ; *Metabolomics ; *Microbiota ; Bacteria/metabolism/genetics/classification ; Metagenomics ; Methane/metabolism ; Thermodynamics ; Multiomics ; },
abstract = {BACKGROUND: Microbial anaerobic metabolism is a key driver of biogeochemical cycles, influencing ecosystem function and health of both natural and engineered environments. However, the temporal dynamics of the intricate interactions between microorganisms and the organic metabolites are still poorly understood. Leveraging metagenomic and metabolomic approaches, we unveiled the principles governing microbial metabolism during a 96-day anaerobic bioreactor experiment.<br><br>RESULTS: During the turnover and assembly of metabolites, homogeneous selection was predominant, peaking at 84.05% on day 12. Consistent dynamic coordination between microbes and metabolites was observed regarding their composition and assembly processes. Our findings suggested that microbes drove deterministic metabolite turnover, leading to consistent molecular conversions across parallel reactors. Moreover, due to the more favorable thermodynamics of N-containing organic biotransformations, microbes preferentially carried out sequential degradations from N-containing to S-containing compounds. Similarly, the metabolic strategy of C18 lipid-like molecules could switch from synthesis to degradation due to nutrient exhaustion and thermodynamical disadvantage. This indicated that community biotransformation thermodynamics emerged as a key regulator of both catabolic and synthetic metabolisms, shaping metabolic strategy shifts at the community level. Furthermore, the co-occurrence network of microbes-metabolites was structured around microbial metabolic functions centered on methanogenesis, with CH4 as a network hub, connecting with 62.15% of total nodes as 1st and 2nd neighbors. Microbes aggregate molecules with different molecular traits and are modularized depending on their metabolic abilities. They established increasingly positive relationships with high-molecular-weight molecules, facilitating resource acquisition and energy utilization. This metabolic complementarity and substance exchange further underscored the cooperative nature of microbial interactions.<br><br>CONCLUSIONS: All results revealed three key rules governing microbial anaerobic degradation. These rules indicate that microbes adapt to environmental conditions according to their community-level metabolic trade-offs and synergistic metabolic functions, further driving the deterministic dynamics of molecular composition. This research offers valuable insights for enhancing the prediction and regulation of microbial activities and carbon flow in anaerobic environments. Video Abstract.},
}
@article {pmid39244357,
year = {2024},
author = {Abo-Ismail, M and Sadek, MAA and Humagain, K and Banjara, N and Pokharel, S},
title = {Spatiotemporal distribution of environmental microbiota around animal farms adjacent to produce fields in central coast California.},
journal = {Food microbiology},
volume = {124},
number = {},
pages = {104598},
doi = {10.1016/j.fm.2024.104598},
pmid = {39244357},
issn = {1095-9998},
mesh = {Animals ; *Bacteria/classification/genetics/isolation &amp; purification ; *Microbiota ; *Seasons ; *Soil Microbiology ; *Farms ; California ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Water Microbiology ; Spatio-Temporal Analysis ; Metagenomics ; },
abstract = {This study aimed to identify different environmental microbiota in animal farms adjacent to produce fields and to understand their potential flow pattern. Soil and water samples were collected from 16 locations during the winter, spring, summer, and fall seasons. In addition, a high-resolution digital elevation model helped to create a stream network to understand the potential flow of the microbiome. Metagenomic analysis of the 16 S rRNA gene revealed that soil and water samples from the four seasons harbor diverse microbiome profiles. The phylogenetic relationship of operational taxonomic units (OTUs) is separated by a maximum of 0.6 Bray-Curtis distance. Similarly, the Principal Component Analysis (P = 0.001) demonstrated the soil and water microbiome clustering across different locations and seasons. The relative abundance of Proteobacteria, Bacteroidetes, and Firmicutes was higher in the water samples than in the soil samples. In contrast, the relative abundance of Actinobacteria and Chloroflexi was higher in the soil compared to the water samples. Soil samples in summer and water samples in spring had the highest abundance of Bacteroidetes and Firmicutes, respectively. A unique microbial community structure was found in water samples, with an increased abundance of Hydrogenophaga and Solirubrobacter. Genera that were significantly abundant at a 1% false discovery rate (FDR) among seasons and soil or water samples, include Nocardioides, Gemmatimonas, JG30-KF-CM45, Massilia, Gaiellales, Sphingomonas, KD4-96, Bacillus, Streptomyces, Gaiella, and Gemmatimonadaceae. The relative abundance of pathogenic genera, including Mycobacterium, Bacteroides, Nocardia, Clostridium, and Corynebacterium, were significantly (at 1% FDR) affected by seasons and environmental type. The elevation-based stream network model suggests the potential flow of microbiomes from the animal farm to the produce fields.},
}
@article {pmid39244165,
year = {2024},
author = {Choi, MH and Kim, D and Lee, KH and Kim, HJ and Sul, WJ and Jeong, SH},
title = {Dysbiosis of the gut microbiota is associated with in-hospital mortality in patients with antibiotic-associated diarrhoea: a metagenomic analysis.},
journal = {International journal of antimicrobial agents},
volume = {},
number = {},
pages = {107330},
doi = {10.1016/j.ijantimicag.2024.107330},
pmid = {39244165},
issn = {1872-7913},
abstract = {BACKGROUND: The increasing incidence of antibiotic-associated diarrhoea (AAD) is a serious health care problem. Dysbiosis of the gut microbiota is suspected to play a role in the pathogenesis of AAD, but its impact on the clinical outcomes of patients remains unclear.<br><br>METHODS: Between May and October 2022, 210 patients with AAD admitted to a university hospital and 100 healthy controls were recruited. DNA extraction from stool specimens and shotgun sequencing were performed. Machine learning was conducted to assess profiling at different taxonomic levels and to select variables for multivariable analyses.<br><br>RESULTS: Patients were classified into two groups: Clostridioides difficile infection (CDI, n&#x202f;=&#x202f;39) and non-CDI AAD (n&#x202f;=&#x202f;171). The in-hospital mortality rate for the patients was 20.0%, but the presence of C. difficile in the gut microbiota was not associated with mortality. Machine learning showed that taxonomic profiling at the genus level best reflected patient prognosis. The in-hospital mortality of patients was associated with the relative abundance of specific gut microbial genera rather than alpha-diversity: each of the five genera correlated either positively (Enterococcus, Klebsiella, Corynebacterium, Pseudomonas, and Anaerofustis) or negatively (Bifidobacterium, Bacteroides, Streptococcus, Faecalibacterium, and Dorea). Genes for vancomycin resistance were significantly associated with in-hospital mortality in patients with AAD (adjusted hazard ratios, 2.45; 95% CI, 1.20-4.99).<br><br>CONCLUSION: This study demonstrates the potential utility of metagenomic studies of the gut microbial community as a biomarker for prognosis prediction in AAD patients.},
}
@article {pmid39244052,
year = {2024},
author = {Wang, Q and Chen, J and Qi, W and Bai, Y and Mao, J and Qu, J},
title = {Dam construction alters the traits of health-related microbes along the Yangtze River.},
journal = {The Science of the total environment},
volume = {953},
number = {},
pages = {176077},
doi = {10.1016/j.scitotenv.2024.176077},
pmid = {39244052},
issn = {1879-1026},
abstract = {Dams, constructed globally for energy production and water conservation, fragment rivers, and modify flow regimes, thereby altering the composition of biological communities and ecosystem functions. Despite the extensive use of dams, few studies have explored their potential health impacts, particularly concerning changes in health-related genes, such as antibiotic resistance genes (ARGs) and virulence factor genes (VFGs), and their hosts (i.e., ARB and potential pathogens). Understanding these health-related effects is crucial because they can impact human health through water quality and pathogen prevalence. In this study, we investigated the planktonic microbial community in the Three Gorges Reservoir (TGR) and adjacent upstream and downstream areas of the Yangtze River during both the dry and wet season. Our metagenomic analysis showed that dam construction significantly decreased the abundance of ARGs, but it had an insignificant effect on VFGs. The observed reduction in ARGs abundance could be mainly attributed to the decrease abundance of the major ARGs carrier - Limnohabitansin the TGR and downstream areas due to high grazing pressure and fitness cost. Conversely, the abundance of microbes carrying VFGs (potential pathogens) remained stable from upstream to the dam reservoir, which may explain the negligible impact on VFG abundance. Overall, our results provide a detailed understanding of the ecological health implications of dam construction in large river ecosystems.},
}
@article {pmid39244041,
year = {2024},
author = {Su, Y and Rahaman, MH and Liu, W and Wen, Y and Zhai, J},
title = {Methane oxidation driven by multiple electron acceptors in the water level fluctuation zone of the Three Gorges Reservoir area, China.},
journal = {The Science of the total environment},
volume = {953},
number = {},
pages = {176041},
doi = {10.1016/j.scitotenv.2024.176041},
pmid = {39244041},
issn = {1879-1026},
abstract = {Water level fluctuations in China's Three Gorges Reservoir (TGR) area are typical of many reservoirs and significantly impact water level fluctuation zones (WLFZ), including upstream rivers. Understanding methane oxidation in the TGR-WLFZ is crucial for evaluating the impact of large-scale reservoir construction on global climate change. In this study, we investigated methane oxidation rates in the TGR-WLFZ, focusing on periods of drying and flooding. The highest methane oxidation rates were observed during the drying period, ranging from 35.69 to 56.32 nmol/(g soil)/d, while the lowest rates were recorded during the flooding period, at 11.58 to 11.98 nmol/(g soil)/d, in lab-scale simulated columns. Using [13]CH4 labeling experiments, we measured CH4 oxidation potentials for aerobic methane oxidation (AMO) using oxygen and anaerobic oxidation of methane (AOM) using nitrite, nitrate, sulfate, ferric iron, and manganese oxide as electron acceptors at varying concentrations. AMO was the dominant process across all experiments, with potentials ranging from 145.71 to 180.77 nmol [13]CO2/(g soil)/d. For AOM, metal-dependent oxidation, particularly with Fe (III) and Mn(IV), was predominant (12.64-17.59 and 3.91-12.69 nmol [13]CO2/(g soil)/d, respectively), followed by nitrite and nitrate-dependent pathways (1.49-9.10 nmol [13]CO2/(g soil)/d). Sulfate-dependent AOM was limited (1.33-3.27 nmol [13]CO2/(g soil)/d). Metagenomic analysis identified key microorganisms responsible for AMO, such as unclassified_f_Methylobacteriaeae and Methylobacterium sp., and for AOM are Ca. Methylomirabilis oxyfera, Ca. Methanoperedens nitroreducens and Ca. Methylomirabilis sp. Complete functional genes and enzymes for the methane oxidation and reverse methanogenesis pathways were obtained in each hydrological period, with the highest content during the drying period and the lowest during flooding. Our study shows that reservoirs, traditionally considered significant sources of methane, may also act as methane sinks. This finding raises new questions: How do different methane oxidation pathways respond to water level fluctuations in reservoirs, and are some pathways more resilient to changes in hydrological conditions?},
}
@article {pmid39243646,
year = {2024},
author = {Liu, P and Guo, Z and Wang, Y and He, M and Kang, Y and Wu, H and Hu, Z and Zhang, J},
title = {Occurrence of polycyclic aromatic hydrocarbons in the Yellow River delta: Sources, ecological risks, and microbial response.},
journal = {Journal of environmental management},
volume = {370},
number = {},
pages = {122432},
doi = {10.1016/j.jenvman.2024.122432},
pmid = {39243646},
issn = {1095-8630},
abstract = {This research investigated the distribution, sources, and ecological risks of polycyclic aromatic hydrocarbons (PAHs) in the Yellow River Delta (YRD), China, emphasizing the response of soil microorganisms. The study involved quantitative analyses of 16 PAHs specified by the U.S. Environmental Protection Agency (USEPA) in both water and soil, utilizing metagenomic technique to determine the response of microbial communities and metabolism within the soil. Results noted that PAHs in the water mainly originate from pyrogenic source and in the soil originate from mixture source, with higher concentrations found in wetland areas compared to river regions. The ecological risk assessment revealed low-to-moderate risk. Microbial analysis demonstrated increased diversity and abundance of bacteria associated with PAHs in areas with higher PAHs pollution. Metagenomic insights revealed significant effects of organic carbon on PAHs degradation genes (ko00624 and ko00626), as well as significant differences in specific metabolic pathways including phenanthrene degradation, with key enzymes showing significant differences between the two environments. The study underscores the importance of understanding PAHs distribution and microbial responses to effectively manage and mitigate pollution in estuarine environments.},
}
@article {pmid39243610,
year = {2024},
author = {Jiang, L and Shen, S and Zuo, A and Chi, Y and Lu, Y and He, Q},
title = {Characterizing flavor development in low-salt Chinese horse bean-chili paste through integrated metabolomics and metagenomics.},
journal = {Food chemistry},
volume = {463},
number = {Pt 1},
pages = {141076},
doi = {10.1016/j.foodchem.2024.141076},
pmid = {39243610},
issn = {1873-7072},
abstract = {This study utilized metabolomics and metagenomics to investigate the microbial composition and functions in low- and high-salt Chinese horse bean-chili pastes (CHCPs). The results showed that 25 key metabolites were identified to distinguish the flavor attributes between the two samples. Leuconostoc was identified as the dominant microbiota in low-salt CHCP, while Pantoea prevailed in the high-salt CHCP. Compared to traditional high-salt fermentation, low-salt and inoculated fermentation promoted the increase in the relative abundances of Companionlactobacillus, Levilactobacillus, Tetragenococcus, Zygosaccharomyces and Wickerhamiella as well as the enrichment of carbohydrate and amino acid metabolic pathways, which contributed to the enhancement of characteristic flavor compounds. Further metabolic pathway reconstruction elucidated 21 potential microbial genera associated with the formation of key metabolites, such as Leuconostoc, Levilactobacillus, Pantoea, and Pectobacterium. This study may provide insights for optimizing the fermentation process and improving the flavor quality of low-salt CHCP and similar fermentation products. KEYWORDS: Low-salt fermentation Hight-salt fermentation Chinese horse-bean chili paste Flavor formation Metabolomics Metagenomics.},
}
@article {pmid39243538,
year = {2024},
author = {Lin, L and Li, L and Yang, X and Hou, L and Wu, D and Wang, B and Ma, B and Liao, X and Yan, X and Gad, M and Su, J and Liu, Y and Liu, K and Hu, A},
title = {Unnoticed antimicrobial resistance risk in Tibetan cities unveiled by sewage metagenomic surveillance: Compared to the eastern Chinese cities.},
journal = {Journal of hazardous materials},
volume = {479},
number = {},
pages = {135730},
doi = {10.1016/j.jhazmat.2024.135730},
pmid = {39243538},
issn = {1873-3336},
mesh = {*Sewage/microbiology ; Tibet ; China ; *Cities ; *Metagenomics ; Drug Resistance, Microbial/genetics ; Bacteria/genetics/drug effects ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; },
abstract = {Sewage surveillance is a cost-effective tool for assessing antimicrobial resistance (AMR) in urban populations. However, research on sewage AMR in remote areas is still limited. Here, we used shotgun metagenomic sequencing to profile antibiotic resistance genes (ARGs) and ARG-carrying pathogens (APs) across 15 cities in Tibetan Plateau (TP) and the major cities in eastern China. Notable regional disparities in sewage ARG composition were found, with a significantly higher ARG abundance in TP (2.97 copies/cell). A total of 542 and 545 APs were identified in sewage from TP and the East, respectively, while more than 40 % carried mobile genetic elements (MGEs). Moreover, 65 MGEs-carrying APs were identified as World Health Organization (WHO) priority-like bacterial and fungal pathogens. Notably, a fungal zoonotic pathogen, Enterocytozoon bieneusi, was found for the first time to carry a nitroimidazole resistance gene (nimJ). Although distinct in AP compositions, the relative abundances of APs were comparable in these two regions. Furthermore, sewage in TP was found to be comparable to the cities in eastern China in terms of ARG mobility and AMR risks. These findings provide insights into ARGs and APs distribution in Chinese sewage and stress the importance of AMR surveillance and management strategies in remote regions.},
}
@article {pmid39243471,
year = {2024},
author = {Cai, M and Zhang, H and Zheng, L and Tang, X},
title = {A global microbiome analysis reveals the ecological feature of Tistrella and its production of the bioactive didemnins in the marine ecosystem.},
journal = {Marine pollution bulletin},
volume = {207},
number = {},
pages = {116939},
doi = {10.1016/j.marpolbul.2024.116939},
pmid = {39243471},
issn = {1879-3363},
mesh = {*Microbiota ; *Ecosystem ; Aquatic Organisms ; Metagenomics ; Seawater/microbiology/chemistry ; },
abstract = {Marine microorganisms like Tistrella are essential for producing bioactive compounds, including didemnins with antitumor and antiviral properties. However, our understanding of Tistrella's ecological features and didemnin production in natural environments is limited. In this study, we used genomics and metagenomics to show that Tistrella is widely distributed across natural habitats, especially in marine environments from the surface to 5000 m deep, with distinct non-random distribution patterns revealed by co-occurrence analysis. Importantly, transcriptional profiling of didemnin biosynthetic gene clusters indicates active in situ production of this compound within marine ecosystems. These findings enhance our understanding of Tistrella's ecology and secondary metabolite production in natural environments. Further research is needed to explore the ecological dynamics and functional impacts of Tistrella in these ecosystems.},
}
@article {pmid39243463,
year = {2024},
author = {Ren, M and Hu, A and Zhang, L and Yao, X and Zhao, Z and Kimirei, IA and Wang, J},
title = {Acidic proteomes are linked to microbial alkaline preference in African lakes.},
journal = {Water research},
volume = {266},
number = {},
pages = {122393},
doi = {10.1016/j.watres.2024.122393},
pmid = {39243463},
issn = {1879-2448},
abstract = {Microbial amino acid composition (AA) reflects adaptive strategies of cellular and molecular regulations such as a high proportion of acidic AAs, including glutamic and aspartic acids in alkaliphiles. It remains understudied how microbial AA content is linked to their pH adaptation especially in natural environments. Here we examined prokaryotic communities and their AA composition of genes with metagenomics for 39 water and sediments of East African lakes along a gradient of pH spanning from 7.2 to 10.1. We found that Shannon diversity declined with the increasing pH and that species abundance were either positively or negatively associated with pH, indicating their distinct habitat preference in lakes. Microbial communities showed higher acidic proteomes in alkaline than neutral lakes. Species acidic proteomes were also positively correlated with their pH preference, which was consistent across major bacterial lineages. These results suggest selective pressure associated with high pH likely shape microbial amino acid composition both at the species and community levels. Comparative genome analyses further revealed that alkaliphilic microbes contained more functional genes with higher acidic AAs when compared to those in neutral conditions. These traits included genes encoding diverse classes of cation transmembrane transporters, antiporters, and compatible solute transporters, which are involved in cytoplasmic pH homeostasis and osmotic stress defense under high pH conditions. Our results provide the field evidence for the strong relationship between prokaryotic AA composition and their habitat preference and highlight amino acid optimization as strategies for environmental adaptation.},
}
@article {pmid39243461,
year = {2024},
author = {Wu, B and Lin, R and Gu, J and Yuan, H and Murphy, JD},
title = {Biochar confers significant microbial resistance to ammonia toxicity in n-caproic acid production.},
journal = {Water research},
volume = {266},
number = {},
pages = {122367},
doi = {10.1016/j.watres.2024.122367},
pmid = {39243461},
issn = {1879-2448},
abstract = {Microbial chain elongation integrating innovative bioconversion technologies with organic waste utilization can transition current energy-intensive n-caproic acid production to sustainable circular bioeconomy systems. However, ammonia-rich waste streams, despite their suitability, pose inhibitory challenges to these bioconversion processes. Herein, biochar was employed as an additive to enhance the activity of chain elongating microbes under ammonia inhibition conditions, with an objective to detail underlying mechanisms of improvements. Biochar addition significantly improved chain elongation performance even under severe ammonia stress (exceeding 8 g N/L), increasing n-caproic acid yields by 40 % to 158 % and reducing lag times by 51 % to 90 %, compared with the best-performing group without biochar addition. The material contribution to n-caproic production reached up to 94.3 % (at 4 g N/L). These enhancements were mainly attributed to the new electron syntrophy induced by biochar, which improved electron transfer system activity and electrical conductivity of the fermentation system. This is further substantiated by increased relative abundances of the genus Sporanaerobacter, electroactive bacteria, and up-regulated direct electron transfer-related genes including conductive pili and c-type cytochrome. This study demonstrates that biochar can confer robust resilience to ammonia toxicity in functional microbes, paving a way for efficient and sustainable n-caproic acid production.},
}
@article {pmid39243135,
year = {2024},
author = {Shi, K and Liu, X and Duan, Y and Ding, J and Jia, Y and Jiang, Z and Feng, C},
title = {Multi-omics analysis reveals associations between host gene expression, gut microbiota and metabolites in chickens.},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skae263},
pmid = {39243135},
issn = {1525-3163},
abstract = {Egg-laying is an important trait in chickens, and it is affected by many factors, such as hormones regulated by the hypothalamic-pituitary axis and precursors synthesized by the liver. Recent studies showed that gut microbiota was associated with egg-laying, however, its underlying mechanism remains unclear. We comprehensively analyzed the host transcriptome, gut microbiota and metabolome in broiler breeder hens during the pre-laying, peak-laying and late-laying periods. The transcriptome analysis of the tissues related to the hypothalamic-pituitary-liver (HPL) axis revealed dynamic gene expression during egg-laying periods. Differentially expressed genes (DEGs) (i.e., PENK, NPY, AVP, PRL, RLN3, and FST) from the hypothalamus and pituitary gland were involved in female gonadal development, hormone secretion, response to endogenous stimulus, liver development, and amide metabolism. In liver, DEGs (i.e., FABP3, VTG1, LPL, APOA5, APOV1, and RBP5) were enriched in efferocytosis, sphingolipid metabolism, amide and peptide biosynthesis. Alpha and beta diversity changed significantly in cecum microbiota during different laying periods. The abundance of Firmicutes was decreased and the abundance of Bacteroidota was increased during the peak-laying period. Functional analysis showed that the biosynthesis of secondary metabolites, amino acids, purine, and steroid hormones were altered during laying. The metabolome analysis from cecal contents showed that amino acid metabolism and steroid hormone biosynthesis changed during laying. Integrated analysis of the cecal microbiota and metabolites showed the genus Megasphaera was involved in amino acid metabolism, which included 3-phenyllatic acid, quinic acid, caffeic acid, and folic acid, and the genus Hungatella participated in steroid hormone biosynthesis through its strong correlation with estradiol. These results explored the dynamic changes in tissues related to the HPL axis and cecal microbiota, and provided new insights into the interaction between the host and microbiota during egg-laying in chickens.},
}
@article {pmid39242818,
year = {2024},
author = {Porras, M&#xc1;G and Assié, A and Tietjen, M and Violette, M and Kleiner, M and Gruber-Vodicka, H and Dubilier, N and Leisch, N},
title = {An intranuclear bacterial parasite of deep-sea mussels expresses apoptosis inhibitors acquired from its host.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {39242818},
issn = {2058-5276},
support = {340535//EC | EC Seventh Framework Programm | FP7 Ideas: European Research Council (FP7-IDEAS-ERC - Specific Programme: "Ideas" Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013))/ ; 340535//EC | EC Seventh Framework Programm | FP7 Ideas: European Research Council (FP7-IDEAS-ERC - Specific Programme: "Ideas" Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013))/ ; 340535//EC | EC Seventh Framework Programm | FP7 Ideas: European Research Council (FP7-IDEAS-ERC - Specific Programme: "Ideas" Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013))/ ; 340535//EC | EC Seventh Framework Programm | FP7 Ideas: European Research Council (FP7-IDEAS-ERC - Specific Programme: "Ideas" Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013))/ ; Gottfried Wilhelm Leibniz Prize//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; Heisenberggrant GR 5028/1-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; OIA 1934844//National Science Foundation (NSF)/ ; IOS 2003107//National Science Foundation (NSF)/ ; },
abstract = {A limited number of bacteria are able to colonize the nuclei of eukaryotes. 'Candidatus Endonucleobacter' infects the nuclei of deep-sea mussels, where it replicates to ≥80,000 bacteria per nucleus and causes nuclei to swell to 50 times their original size. How these parasites are able to replicate and avoid apoptosis is not known. Dual RNA-sequencing transcriptomes of infected nuclei isolated using laser-capture microdissection revealed that 'Candidatus Endonucleobacter' does not obtain most of its nutrition from nuclear DNA or RNA. Instead, 'Candidatus Endonucleobacter' upregulates genes for importing and digesting sugars, lipids, amino acids and possibly mucin from its host. It likely prevents apoptosis of host cells by upregulating 7-13 inhibitors of apoptosis, proteins not previously seen in bacteria. Comparative phylogenetic analyses revealed that 'Ca. Endonucleobacter' acquired inhibitors of apoptosis through horizontal gene transfer from their hosts. Horizontal gene transfer from eukaryotes to bacteria is assumed to be rare, but may be more common than currently recognized.},
}
@article {pmid39242817,
year = {2024},
author = {Shao, Y and Garcia-Mauriño, C and Clare, S and Dawson, NJR and Mu, A and Adoum, A and Harcourt, K and Liu, J and Browne, HP and Stares, MD and Rodger, A and Brocklehurst, P and Field, N and Lawley, TD},
title = {Primary succession of Bifidobacteria drives pathogen resistance in neonatal microbiota assembly.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {39242817},
issn = {2058-5276},
support = {WT101169MA, 206194 and 108413/A/15/D//Wellcome Trust (Wellcome)/ ; },
abstract = {Human microbiota assembly commences at birth, seeded by both maternal and environmental microorganisms. Ecological theory postulates that primary colonizers dictate microbial community assembly outcomes, yet such microbial priority effects in the human gut remain underexplored. Here using longitudinal faecal metagenomics, we characterized neonatal microbiota assembly for a cohort of 1,288 neonates from the UK. We show that the pioneering neonatal gut microbiota can be stratified into one of three distinct community states, each dominated by a single microbial species and influenced by clinical and host factors, such as maternal age, ethnicity and parity. A community state dominated by Enterococcus faecalis displayed stochastic microbiota assembly with persistent high pathogen loads into infancy. In contrast, community states dominated by Bifidobacterium, specifically B. longum and particularly B. breve, exhibited a stable assembly trajectory and long-term pathogen colonization resistance, probably due to strain-specific functional adaptions to a breast milk-rich neonatal diet. Consistent with our human cohort observation, B. breve demonstrated priority effects and conferred pathogen colonization resistance in a germ-free mouse model. Our findings solidify the crucial role of Bifidobacteria as primary colonizers in shaping the microbiota assembly and functions in early life.},
}
@article {pmid39242698,
year = {2024},
author = {Lu, X and Gong, G and Zhang, Q and Yang, S and Wu, H and Zhao, M and Wang, X and Shen, Q and Ji, L and Liu, Y and Wang, Y and Liu, J and Suolang, S and Ma, X and Shan, T and Zhang, W},
title = {Metagenomic analysis reveals high diversity of gut viromes in yaks (Bos grunniens) from the Qinghai-Tibet Plateau.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {1097},
pmid = {39242698},
issn = {2399-3642},
mesh = {Animals ; Cattle ; *Metagenomics ; *Gastrointestinal Microbiome/genetics ; *Virome/genetics ; Tibet ; Metagenome ; },
abstract = {The Qinghai-Tibet Plateau (QTP), renowned for its exceptional biological diversity, is home to numerous endemic species. However, research on the virology of vulnerable vertebrates like yaks remains limited. In this study, our objective was to use metagenomics to provide a comprehensive understanding of the diversity and evolution of the gut virome in yak populations across different regions of the QTP. Our findings revealed a remarkably diverse array of viruses in the gut of yaks, including those associated with vertebrates and bacteriophages. Notably, some vertebrate-associated viruses, such as astrovirus and picornavirus, showed significant sequence identity across diverse yak populations. Additionally, we observed differences in the functional profiles of genes carried by the yak gut virome across different regions. Moreover, the virus-bacterium symbiotic network that we discovered holds potential significance in maintaining the health of yaks. Overall, this research expands our understanding of the viral communities in the gut of yaks and highlights the importance of further investigating the interactions between viruses and their hosts. These data will be beneficial for revealing the crucial role that viruses play in the yak gut ecology in future studies.},
}
@article {pmid39242694,
year = {2024},
author = {Oren, A},
title = {Novel insights into the diversity of halophilic microorganisms and their functioning in hypersaline ecosystems.},
journal = {npj biodiversity},
volume = {3},
number = {1},
pages = {18},
pmid = {39242694},
issn = {2731-4243},
abstract = {Our understanding of the microbial diversity inhabiting hypersaline environments, here defined as containing >100-150 g/L salts, has greatly increased in the past five years. Halophiles are found in each of the three domains of life. Many novel types have been cultivated, and metagenomics and other cultivation-independent approaches have revealed the existence of many previously unrecognized lineages. Syntrophic interactions between different phylogenetic lineages have been discovered, such as the symbiosis between members of the archaeal class Halobacteria and the 'Candidatus Nanohalarchaeota'. Metagenomics techniques also have shed light on the biogeography of halophiles, especially of the genera Salinibacter (Bacteria) and Haloquadratum and Halorubrum (Archaea). Exploration of the microbiome of hypersaline lakes led to the discovery of novel types of metabolism previously unknown to occur at high salt concentrations. Studies of environments with high concentrations of chaotropic ions such as magnesium, calcium, and lithium have refined our understanding of the limits of life.},
}
@article {pmid39242568,
year = {2024},
author = {Zhou, T and Wu, J and Khan, A and Hu, T and Wang, Y and Salama, ES and Su, S and Han, H and Jin, W and Li, X},
title = {A probiotic Limosilactobacillus fermentum GR-3 mitigates colitis-associated tumorigenesis in mice via modulating gut microbiome.},
journal = {NPJ science of food},
volume = {8},
number = {1},
pages = {61},
pmid = {39242568},
issn = {2396-8370},
support = {32200080//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Bacterial therapy for colorectal cancer (CRC) represents a burgeoning frontier. The probiotic Limosilactobacillus fermentum GR-3, derived from traditional food "Jiangshui", exhibited superior antioxidant capacity by producing indole derivatives ICA and IPA. In an AOM/DSS-induced CRC mouse model, GR-3 treatment alleviated weight loss, colon shortening, rectal bleeding and intestinal barrier disruption by reducing oxidative stress and inflammation. GR-3 colonization in distant colon induced apoptosis and reduced tumor incidence by 51.2%, outperforming the control strain and vitamin C. The beneficial effect of GR-3 on CRC was associated with gut microbiome modulation, increasing SCFA producer Lachnospiraceae NK4A136 group and suppressing pro-inflammatory strain Bacteroides. Metagenomic and metabolic analyses revealed that GR-3 intervention upregulated antioxidant genes (xseA, ALDH) and butyrate synthesis gene (bcd), while increasing beneficial metabolites (SCFAs, ICA, IPA, VB12 and VD3) and reducing harmful secondary bile acids. Overall, GR-3 emerges as a promising candidate in CRC therapy, offering effective gut microbiome remediation.},
}
@article {pmid39242535,
year = {2024},
author = {Attrah, M and Schärer, MR and Esposito, M and Gionchetta, G and Bürgmann, H and Lens, PNL and Fenner, K and van de Vossenberg, J and Robinson, SL},
title = {Disentangling abiotic and biotic effects of treated wastewater on stream biofilm resistomes enables the discovery of a new planctomycete beta-lactamase.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {164},
pmid = {39242535},
issn = {2049-2618},
support = {109070/WT_/Wellcome Trust/United Kingdom ; Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung, 186531 (ANTIVERSA as part of biodeversa+, European Biodiversity Partnership)//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung, 186531 (ANTIVERSA as part of biodeversa+, European Biodiversity Partnership)//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; 200021L_201006//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; PZPGP2_209124//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; },
mesh = {*Biofilms/drug effects ; *Wastewater/microbiology ; *beta-Lactamases/genetics ; *Rivers/microbiology ; *Metagenomics ; Microbiota/drug effects ; Bacteria/genetics/classification/drug effects/isolation &amp; purification ; Anti-Bacterial Agents/pharmacology ; Planctomycetales/genetics/drug effects ; Metagenome ; Bacterial Proteins/genetics/metabolism ; },
abstract = {BACKGROUND: Environmental reservoirs of antibiotic resistance pose a threat to human and animal health. Aquatic biofilms impacted by wastewater effluent (WW) are known environmental reservoirs for antibiotic resistance; however, the relative importance of biotic factors and abiotic factors from WW on the abundance of antibiotic resistance genes (ARGs) within aquatic biofilms remains unclear. Additionally, experimental evidence is limited within complex aquatic microbial communities as to whether genes bearing low sequence similarity to validated reference ARGs are functional as ARGs.<br><br>RESULTS: To disentangle the effects of abiotic and biotic factors on ARG abundances, natural biofilms were previously grown in flume systems with different proportions of stream water and either ultrafiltered or non-ultrafiltered WW. In this study, we conducted deep shotgun metagenomic sequencing of 75 biofilm, stream, and WW samples from these flume systems and compared the taxonomic and functional microbiome and resistome composition. Statistical analysis revealed an alignment of the resistome and microbiome composition and a significant association with experimental treatment. Several ARG classes exhibited an increase in normalized metagenomic abundances in biofilms grown with increasing percentages of non-ultrafiltered WW. In contrast, sulfonamide and extended-spectrum beta-lactamase ARGs showed greater abundances in biofilms grown in ultrafiltered WW compared to non-ultrafiltered WW. Overall, our results pointed toward the dominance of biotic factors over abiotic factors in determining ARG abundances in WW-impacted stream biofilms and suggested gene family-specific mechanisms for ARGs that exhibited divergent abundance patterns. To investigate one of these specific ARG families experimentally, we biochemically characterized a new beta-lactamase from the Planctomycetota (Phycisphaeraceae). This beta-lactamase displayed activity in the cleavage of cephalosporin analog despite sharing a low sequence identity with known ARGs.<br><br>CONCLUSIONS: This discovery of a functional planctomycete beta-lactamase ARG is noteworthy, not only because it was the first beta-lactamase to be biochemically characterized from this phylum, but also because it was not detected by standard homology-based ARG tools. In summary, this study conducted a metagenomic analysis of the relative importance of biotic and abiotic factors in the context of WW discharge and their impact on both known and new ARGs in aquatic biofilms. Video Abstract.},
}
@article {pmid39241602,
year = {2024},
author = {Zheng, Y and Xu, F and Gan, J and Jin, H and Lou, J},
title = {Impact of operating conditions on N2O accumulation in Nitrate-DAMO system: Kinetics and microbiological analysis.},
journal = {Journal of environmental management},
volume = {369},
number = {},
pages = {122389},
doi = {10.1016/j.jenvman.2024.122389},
pmid = {39241602},
issn = {1095-8630},
mesh = {*Nitrous Oxide/metabolism ; *Nitrates/metabolism ; Kinetics ; *Methane/metabolism ; Oxidation-Reduction ; Anaerobiosis ; Nitrogen/metabolism ; Denitrification ; Bacteria/metabolism ; },
abstract = {Nitrate-dependent anaerobic methane oxidation (Nitrate-DAMO) is a novel and sustainable process that removes both nitrogen and methane. Previously, the metabolic pathway of Nitrate-DAMO has been intensively studied with some results. However, the production and consumption of nitrous oxide (N2O) in the Nitrate-DAMO system were widely disregarded. In this study, a Nitrate-DAMO system was used to investigate the effect of operational parameters (C/N ratio, pH, and temperature) on N2O accumulation, and the optimal operating conditions were determined (C/N = 3, pH = 6.5, and temperature = 20 °C). In this study, an enzyme kinetic model was used to fit the nitrate nitrogen degradation and the nitrous oxide production and elimination under different operating conditions. The thermodynamic model of N2O production and elimination in the system also has been constructed. Multiple linear regression analysis found that pH was the most important factor influencing N2O accumulation. The Metagenomics sequencing results showed that alkaline pH promoted the abundance of Nor genes and denitrifying bacteria, which were significantly and positively correlated with N2O emissions. And alkaline pH also promoted the production of Mdo genes related to the N2O-driven AOM reaction, indicating that part of the N2O was consumed by denitrifying bacteria and the other part was consumed by the N2O-driven AOM reaction. These findings reveal the mechanism of N2O production and consumption in DAMO systems and provide a theoretical basis for reducing N2O production and greenhouse gas emissions in actual operation.},
}
@article {pmid39241588,
year = {2024},
author = {Wang, S and Jiang, T and Hao, X and Dai, Y and Yang, J and Wang, B},
title = {Enhanced and robust nitrogen removal using an integrated zeolite and partial denitrification anammox process.},
journal = {Journal of environmental management},
volume = {369},
number = {},
pages = {122381},
doi = {10.1016/j.jenvman.2024.122381},
pmid = {39241588},
issn = {1095-8630},
mesh = {*Zeolites ; *Denitrification ; *Nitrogen/metabolism ; Bioreactors ; Sewage ; RNA, Ribosomal, 16S/genetics ; Ammonium Compounds/metabolism ; Anaerobiosis ; Waste Disposal, Fluid/methods ; },
abstract = {Anammox has received increased attention due to its enhanced and cost-efficient approach to nitrogen removal. However, its practical application is complicated by strict influent NO2[-]-N to NH4[+]-N ratio demands and an 11% nitrate production from the anammox process. This study was the first known research to propose and verify a system of zeolite integrated with partial denitrification and anammox (Z-PDA) in an up-flow anaerobic sludge bed (UASB) reactor. The enhanced and robust nitrogen removal resulted in an ultra-high nitrogen removal efficiency (NRE, 93.0 ± 2.0%). Zeolite adsorption and biological desorption of ammonium contributed to robust nitrogen removal with fluctuating influent NO2[-]-N to NH4[+]-N ratios. Applying 16S rRNA gene sequencing found that Candidatus Brocadia and Thauera were the key bacteria responsible for anammox and partial denitrification (PD), respectively. Zeolite also acted as a biological carrier. This significantly enriched anammox bacteria with a higher relative abundance of Candidatus Brocadia, reaching 49.2%. Metagenomic analysis demonstrated that the multiple functional genes related to nitrogen removal (nrfA/H, narG/H/I) and the metabolic pathways (Biosynthesis of cofactors, the Two-component system, the Biosynthesis of nucleotide sugars, and Purine metabolism) ensured the resilience of the Z-PDA system despite influent fluctuations. Overall, this study provided novel insights into the impacts of zeolite in the PDA system. It described the fundamental mechanism of zeolite based on adsorption and biological desorption, and demonstrated a meaningful application of the anammox process in sewage treatment.},
}
@article {pmid39241382,
year = {2024},
author = {Hao, S and Zhang, L and Gao, J and Dong, T and Peng, Y and Miyazawa, A},
title = {Genomic synergistic efficient carbon fixation and nitrogen removal induced by excessive inorganic carbon in the anammox-centered coupling system.},
journal = {Water research},
volume = {266},
number = {},
pages = {122366},
doi = {10.1016/j.watres.2024.122366},
pmid = {39241382},
issn = {1879-2448},
abstract = {Given the significance of HCO3[-] for autotrophic anammox bacteria (AnAOB), excessive HCO3[-] was always provided in anammox-related systems and engineering applications. However, its impact mechanism on anammox process at genome-level remains unknown. This study firstly established an anammox-centered coupling system that entails heterotrophic partial denitrification (PD) and hydrolytic acidification (A-PDHA) fed mainly with inorganic carbon (high HCO3[-] concentration and low C/N ratio). Metagenomic binning and metatranscriptomics analyses indicated that high HCO3[-] concentration enhanced expression of natural most efficient phosphoenolpyruvate (PEP) carboxylase within AnAOB, by up to 30.59 folds. This further induced AnAOB to achieve high-speed carbon-fixing reaction through cross-feeding of phosphate and PEP precursors with heterotrophs. Additionally, the enhanced activity of transporters and catalytic enzymes (up to 4949-fold) induced by low C/N ratio enabled heterotrophs to eliminate extracellular accumulated energy precursors mainly derived from carbon fixation products of AnAOB. This maintained high-speed carbon-fixing reaction within AnAOB and supplemented heterotrophs with organics. Moreover, assimilated energy precursors stimulated nitrogen metabolism enzymes, especially NO2[-] reductase (968.14 times), in heterotrophs. This established an energy-saving PD-A process mediated by interspecies NO shuttle. These variation resulted in efficient nitrogen removal (>95 %) and reduced external organic carbon demand (67 %) in A-PDHA system. This study unveils the great potential of an anammox-centered autotrophic-heterotrophic coupling system for achieving cost-effective nitrogen removal and enhancing carbon fixation under excessive HCO3[-] doses.},
}
@article {pmid39241365,
year = {2024},
author = {Zhang, X and Xu, D and Usman, S and Li, Y and Liang, Y and Bai, J and Guo, X},
title = {Heterofermentative Lentilactobacillus buchneri and low dry matter reduce high-risk antibiotic resistance genes in corn silage by regulating pathogens and mobile genetic element.},
journal = {Journal of hazardous materials},
volume = {479},
number = {},
pages = {135700},
doi = {10.1016/j.jhazmat.2024.135700},
pmid = {39241365},
issn = {1873-3336},
mesh = {*Zea mays/microbiology ; *Silage/microbiology ; Genes, Bacterial ; Interspersed Repetitive Sequences ; Drug Resistance, Microbial/genetics ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Lactobacillus/genetics/drug effects ; Fermentation ; },
abstract = {The study of antibiotic resistance in the silage microbiome has attracted initial attention. However, the influences of lactic acid bacteria inoculants and dry matter (DM) content on antibiotic resistance genes (ARGs) reduction in whole-plant corn silage remain poorly studied. This study accessed the ARGs' risk and transmission mechanism in whole-plant corn silage with different DM levels and treated with Lactiplantibacillus plantarum or Lentilactobacillus buchneri. The macrolide and tetracycline were the main ARGs in corn silage. The dominant species (Lent. buchneri and Lactobacillus acetotolerans) were the main ARGs carriers in whole-plant corn silage. The application of Lent. buchneri increased total ARGs abundance regardless of corn DM. Whole-plant corn silage with 30 % DM reduced the abundances of integrase and plasmid compared with 40 % DM. The correlation and structural equation model analysis demonstrated that bacterial community succession, resulting from changes in DM content, was the primary driving factor influencing the ARGs distribution in whole-plant corn silage. Interestingly, whole-plant corn silage inoculated with Lent. buchneri reduced abundances of high-risk ARGs (mdtG, mepA, tetM, mecA, vatE and tetW) by regulating pathogens (Escherichia coli), mobile genetic elements (MGEs) genes (IS3 and IS1182), and this effect was more pronounced at 30 % DM level. In summary, although whole-plant corn silage inoculated with Lent. buchneri increased the total ARGs abundance at both DM levels, it decreased the abundance of high-risk ARGs by reducing the abundances of the pathogens and MGEs, and this effect was more noticeable at 30 % DM level.},
}
@article {pmid39241334,
year = {2024},
author = {Ouyang, B and Yang, C and Lv, Z and Chen, B and Tong, L and Shi, J},
title = {Recent advances in environmental antibiotic resistance genes detection and research focus: From genes to ecosystems.},
journal = {Environment international},
volume = {191},
number = {},
pages = {108989},
doi = {10.1016/j.envint.2024.108989},
pmid = {39241334},
issn = {1873-6750},
mesh = {*Drug Resistance, Microbial/genetics ; *Ecosystem ; Metagenomics/methods ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Environmental Microbiology ; Environmental Monitoring/methods ; },
abstract = {Antibiotic resistance genes (ARGs) persistence and potential harm have become more widely recognized in the environment due to its fast-paced research. However, the bibliometric review on the detection, research hotspot, and development trend of environmental ARGs has not been widely conducted. It is essential to provide a comprehensive overview of the last 30 years of research on environmental ARGs to clarify the changes in the research landscape and ascertain future prospects. This study presents a visualized analysis of data from the Web of Science to enhance our understanding of ARGs. The findings indicate that solid-phase extraction provides a reliable method for extracting ARG. Technological advancements in commercial kits and microfluidics have facilitated the efficacy of ARGs extraction with significantly reducing processing times. PCR and its derivatives, DNA sequencing, and multi-omics technology are the prevalent methodologies for ARGs detection, enabling the expansion of ARG research from individual strains to more intricate microbial communities in the environment. Furthermore, due to the development of combination, hybridization and mass spectrometer technologies, considerable advancements have been achieved in terms of sensitivity and accuracy as well as lowering the cost of ARGs detection. Currently, high-frequency terms such as "Antibiotic Resistance, Antibiotics, and Metagenomics" are the center of attention for study in this area. Prominent topics include the investigation of anthropogenic impacts on environmental resistance, as well as the dynamics of migration, dissemination, and adaptation of environmental ARGs, etc. The research on environmental ARGs has made significant advancements in the fields of "Microbiology" and "Biotechnology Applied Microbiology". Over the past decade, there has been a notable increase in the fields of "Environmental Sciences Ecology" and "Engineering" with a similar growth trend observed in "Water Resources". These three domains are expected to continue driving extensive study within the realm of environmental ARGs.},
}
@article {pmid39240096,
year = {2024},
author = {Ruiz-Perez, D and Gimon, I and Sazal, M and Mathee, K and Narasimhan, G},
title = {Unfolding and de-confounding: biologically meaningful causal inference from longitudinal multi-omic networks using METALICA.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0130323},
doi = {10.1128/msystems.01303-23},
pmid = {39240096},
issn = {2379-5077},
abstract = {UNLABELLED: A key challenge in the analysis of microbiome data is the integration of multi-omic datasets and the discovery of interactions between microbial taxa, their expressed genes, and the metabolites they consume and/or produce. In an effort to improve the state of the art in inferring biologically meaningful multi-omic interactions, we sought to address some of the most fundamental issues in causal inference from longitudinal multi-omics microbiome data sets. We developed METALICA, a suite of tools and techniques that can infer interactions between microbiome entities. METALICA introduces novel unrolling and de-confounding techniques used to uncover multi-omic entities that are believed to act as confounders for some of the relationships that may be inferred using standard causal inferencing tools. The results lend support to predictions about biological models and processes by which microbial taxa interact with each other in a microbiome. The unrolling process helps identify putative intermediaries (genes and/or metabolites) to explain the interactions between microbes; the de-confounding process identifies putative common causes that may lead to spurious relationships to be inferred. METALICA was applied to the networks inferred by existing causal discovery, and network inference algorithms were applied to a multi-omics data set resulting from a longitudinal study of IBD microbiomes. The most significant unrollings and de-confoundings were manually validated using the existing literature and databases.<br><br>IMPORTANCE: We have developed a suite of tools and techniques capable of inferring interactions between microbiome entities. METALICA introduces novel techniques called unrolling and de-confounding that are employed to uncover multi-omic entities considered to be confounders for some of the relationships that may be inferred using standard causal inferencing tools. To evaluate our method, we conducted tests on the inflammatory bowel disease (IBD) dataset from the iHMP longitudinal study, which we pre-processed in accordance with our previous work. From this dataset, we generated various subsets, encompassing different combinations of metagenomics, metabolomics, and metatranscriptomics datasets. Using these multi-omics datasets, we demonstrate how the unrolling process aids in the identification of putative intermediaries (genes and/or metabolites) to explain the interactions between microbes. Additionally, the de-confounding process identifies potential common causes that may give rise to spurious relationships to be inferred. The most significant unrollings and de-confoundings were manually validated using the existing literature and databases.},
}
@article {pmid39240085,
year = {2024},
author = {Cheng, L-l and Li, Z-t and Wu, H-k and Li, F and Qiu, Y and Wang, T and Peng, H and Liu, Z-h and Huang, P-r and Zhou, L and Gao, L-f and Huang, H-j and Zhang, B and Deng, X-l and Chen, X and Ye, F and Liu, X-q and Guan, W-j and Li, Y-p and Li, Y-m and Li, S-y and Zhong, N-s},
title = {Clinical and pathogen features of COVID-19-associated infections during an Omicron strain outbreak in Guangzhou, China.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0340623},
doi = {10.1128/spectrum.03406-23},
pmid = {39240085},
issn = {2165-0497},
abstract = {UNLABELLED: Although the Omicron variant has been associated with greater transmissibility and tropism of the upper respiratory tract, the clinical and pathogenic features of patients infected with the Omicron variant during an outbreak in China have been unclear. Adults with COVID-19 were retrospectively enrolled from seven medical centers in Guangzhou, China, and clinical information and specimens (BALF, sputum, and throat swabs) from participants were collected. Conventional detection methods, metagenomics next-generation sequencing (mNGS), and other methods were used to detect pathogens in lower respiratory tract samples. From December 2022 to January 2023, we enrolled 836 patients with COVID-19, among which 56.7% patients had severe/critical illness. About 91.4% of patients were infected with the Omicron strain (BA.5.2). The detection rate of possible co-infection pathogens was 53.4% by mNGS, including Klebsiella pneumoniae (16.3%), Aspergillus fumigatus (12.2%), and Pseudomonas aeruginosa (11.8%). The co-infection rate was 19.5%, with common pathogens being Streptococcus pneumoniae (11.5%), Haemophilus influenzae (9.2%), and Adenovirus (6.9%). The superinfection rate was 75.4%, with common pathogens such as Klebsiella pneumoniae (26.1%) and Pseudomonas aeruginosa (19.4%). Klebsiella pneumoniae (27.1%% vs 6.1%, P < 0.001), Aspergillus fumigatus (19.6% vs 5.3%, P = 0.001), Acinetobacter baumannii (18.7% vs 4.4%, P = 0.001), Pseudomonas aeruginosa (16.8% vs 7.0%, P = 0.024), Staphylococcus aureus (14.0% vs 5.3%, P = 0.027), and Streptococcus pneumoniae (0.9% vs 10.5%, P = 0.002) were more common in severe cases. Co-infection and superinfection of bacteria and fungi are common in patients with severe pneumonia associated with Omicron variant infection. Sequencing methods may aid in the diagnosis and differential diagnosis of pathogens.<br><br>IMPORTANCE: Our study has analyzed the clinical characteristics and pathogen spectrum of the lower respiratory tract associated with co-infection or superinfection in Guangzhou during the outbreak of the Omicron strain, particularly after the relaxation of the epidemic prevention and control strategy in China. This study will likely prompt further research into the specific issue, which will benefit clinical practice.},
}
@article {pmid39240026,
year = {2024},
author = {Sheldon, RA},
title = {Waste Valorization in a Sustainable Bio-Based Economy: The Road to Carbon Neutrality.},
journal = {Chemistry (Weinheim an der Bergstrasse, Germany)},
volume = {},
number = {},
pages = {e202402207},
doi = {10.1002/chem.202402207},
pmid = {39240026},
issn = {1521-3765},
abstract = {The development of sustainable chemistry underlying the quest to minimize and/or valorize waste in the carbon-neutral manufacture of chemicals is followed over the last four to five decades. Both chemo- and biocatalysis have played an indispensable role in this odyssey. in particular developments in protein engineering, metagenomics and bioinformatics over the preceding three decades have played a crucial supporting role in facilitating the widespread application of both whole cell and cell-free biocatalysis. The pressing need, driven by climate change mitigation, for a drastic reduction in greenhouse gas (GHG) emissions, has precipitated an energy transition based on decarbonization of energy and defossilization of organic chemicals production. The latter involves waste biomass and/or waste CO2 as the feedstock and green electricity generated using solar, wind, hydroelectric or nuclear energy. The use of waste polysaccharides as feedstocks will underpin a renaissance in carbohydrate chemistry with pentoses and hexoses as base chemicals and bio-based solvents and polymers as environmentally friendly downstream products. The widespread availability of inexpensive electricity and solar energy has led to increasing attention for electro(bio)catalysis and photo(bio)catalysis which in turn is leading to myriad innovations in these fields.},
}
@article {pmid39239875,
year = {2024},
author = {Kwan, SY and Gonzales, KA and Jamal, MA and Stevenson, HL and Tan, L and Lorenzi, PL and Futreal, PA and Hawk, ET and McCormick, JB and Fisher-Hoch, SP and Jenq, RR and Beretta, L},
title = {Protection against fibrosis by a bacterial consortium in metabolic dysfunction-associated steatohepatitis and the role of amino acid metabolism.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2399260},
pmid = {39239875},
issn = {1949-0984},
support = {P30 CA016672/CA/NCI NIH HHS/United States ; P50 CA217674/CA/NCI NIH HHS/United States ; UL1 TR000371/TR/NCATS NIH HHS/United States ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; Humans ; *Liver Cirrhosis/microbiology/metabolism ; Mice ; *Amino Acids/metabolism ; *Bacteria/classification/metabolism/genetics/isolation &amp; purification ; Male ; *Liver/metabolism/pathology/microbiology ; Female ; Feces/microbiology ; Mice, Inbred C57BL ; Middle Aged ; Fatty Liver/metabolism/microbiology ; Disease Models, Animal ; Metagenome ; Adult ; },
abstract = {The gut microbiota drives progression to liver fibrosis, the main determinant of mortality in metabolic dysfunction-associated steatohepatitis (MASH). In this study, we aimed to identify bacterial species associated with protection against liver fibrosis in a high-risk population, and test their potential to protect against liver fibrosis in vivo. Based on stool shotgun metagenomic sequencing of 340 subjects from a population cohort disproportionally affected by MASH, we identified bacterial species from the Bacteroidales and Clostridiales orders associated with reduced risk of liver fibrosis. A bacterial consortium was subsequently tested in a mouse model of MASH, which demonstrated protective effects against liver fibrosis. Six of the eight inoculated bacteria were detected in mouse stool and liver. Intrahepatic presence of bacteria was further confirmed by bacterial culture of mouse liver tissue. Changes in liver histological parameters, gut functional profiles, and amino acid profiles were additionally assessed. Comparison between fibrosis-associated human metagenome and bacteria-induced metagenome changes in mice identified microbial functions likely to mediate the protective effect against liver fibrosis. Amino acid profiling confirmed an increase in cysteine synthase activity, associated with reduced fibrosis. Other microbiota-induced changes in amino acids associated with reduced fibrosis included increased gut asparaginase activity and decreased hepatic tryptophan-to-kynurenine conversion. This human-to-mouse study identified bacterial species and their effects on amino acid metabolism as innovative strategies to protect against liver fibrosis in MASH.},
}
@article {pmid39239243,
year = {2024},
author = {Ma, R and Wang, YM and Guan, H and Zhang, L and Zhang, W and Chen, LC},
title = {Pulmonary abscess caused by Streptococcus pseudopneumoniae in a child: A case report and review of literature.},
journal = {World journal of radiology},
volume = {16},
number = {8},
pages = {362-370},
pmid = {39239243},
issn = {1949-8470},
abstract = {BACKGROUND: Lung abscess found on chest X-ray and computed tomography examinations is rare in infants and young children. Several pathogens can cause lung abscesses, with the most common pathogens being anaerobes, Streptococci and Staphylococcus aureus. Streptococcus pseudopneumoniae (S. pseudopneumoniae) is a member of the Streptococcaceae family, and is mainly isolated from respiratory tract specimens. There are currently no cases of lung abscess caused by S. pseudopneumoniae in the literature.<br><br>CASE SUMMARY: A 2-year-old boy was admitted to hospital due to persistent cough and fever. Lung computed tomography examination suggested the formation of a lung abscess. His diagnosis was not confirmed by testing for serum respiratory pathogens (6 items), respiratory pathogen nucleic acid (27 items), and laboratory culture. Finally, metagenomic next-generation sequencing of bronchoalveolar lavage fluid revealed the presence of S. pseudopneumoniae, confirming its role in causing the lung abscess. After receiving antibiotic treatment, reexamination with lung computed tomography showed that the abscess was resorbed and the patient's outcome was good.<br><br>CONCLUSION: This is the first report of a lung abscess in a child caused by S. pseudopneumoniae infection. Metagenomic next-generation sequencing of bronchoalveolar lavage fluid is helpful in achieving rapid and accurate pathogen identification.},
}
@article {pmid39239090,
year = {2024},
author = {Haidar, G and Kline, EG and Kitsios, GD and Wang, X and Kwak, EJ and Newbrough, A and Friday, K and Hughes Kramer, K and Shields, RK},
title = {Emergence of high-level aztreonam-avibactam and cefiderocol resistance following treatment of an NDM-producing Escherichia coli bloodstream isolate exhibiting reduced susceptibility to both agents at baseline.},
journal = {JAC-antimicrobial resistance},
volume = {6},
number = {5},
pages = {dlae141},
pmid = {39239090},
issn = {2632-1823},
abstract = {BACKGROUND: Cefiderocol (FDC) or ceftazidime-avibactam with aztreonam (CZA-ATM) are frontline agents for New Delhi metallo-β-lactamase (NDM)-producing Enterobacterales; however, clinical data are scarce, and mechanisms of treatment-emergent resistance are ill-defined. Our objectives were to characterize serial isolates and stool microbiota from a liver transplant recipient with NDM-producing Escherichia coli bacteraemia.<br><br>METHODS: Isolates collected pre- and post-CZA-ATM treatment underwent broth microdilution susceptibility testing and whole-genome sequencing. Longitudinal stool collected during CZA-ATM therapy underwent metagenomic sequencing (Nanopore MinION).<br><br>RESULTS: The baseline isolate exhibited elevated MICs for ATM-AVI (16/4&#x2005;&#xb5;g/mL) and FDC (8&#x2005;&#xb5;g/mL). Posttreatment, a rectal surveillance isolate exhibited high-level resistance to ATM-AVI (> 128/4&#x2005;&#xb5;g/mL) and FDC (32&#x2005;&#xb5;g/mL). Both isolates belonged to ST361 and harboured WT bla NDM-5. The baseline isolate contained wild type (WT) bla CMY-145 and mutations in ftsI (which encodes PBP3), including a YRIN insertion at residue 338 and the non-synonymous substitutions Q227H, E353K and I536L. The posttreatment isolate harboured new mutations in ftsI (A417&#x2005;V) and bla CMY-145 (L139R and N366Y). Analysis of four stool samples collected during CZA-ATM treatment revealed high E. coli abundance. E. coli relative abundance increased from 34.5% (first sample) to 61.9% (last sample).<br><br>CONCLUSIONS: Baseline mutations in ftsI were associated with reduced susceptibility to ATM-AVI and FDC in an ST361 NDM-5-producing E. coli bloodstream isolate. High-level resistance was selected after CZA-ATM treatment, resulting in new ftsl and bla CMY-145 mutations. These findings underscore the need for ATM-AVI susceptibility testing for NDM producers, and the potential for PBP3 mutations to confer cross-resistance to ATM-AVI and FDC, which can emerge after CZA-ATM treatment.},
}
@article {pmid39238444,
year = {2024},
author = {Zhang, W and Liu, F and Liang, E and Zhang, L},
title = {Evolution of Treatment Modalities for Disseminated HAdV Infection in Neonates.},
journal = {Pediatrics},
volume = {},
number = {},
pages = {},
doi = {10.1542/peds.2024-066677},
pmid = {39238444},
issn = {1098-4275},
abstract = {Human adenovirus (HAdV) infection in newborns is a rare condition that typically affects multiple organ systems and has a high mortality rate. We report a case of neonatal HAdV-D37 infection that presented with fever and respiratory distress that was confirmed by metagenomic next-generation sequencing using blood and bronchoalveolar lavage fluid. We treated the patient with intravenous immunoglobulin, methylprednisolone, and anticoagulants, and the patient recovered. Our review of 41 cases of HAdV found that treatment with intravenous immunoglobin might have improved the outcome of HAdV-D infection. We further suggest that glucocorticoid therapy may have additional therapeutic validity in the setting of severe or disseminated disease and that monitoring coagulation function and timely anticoagulation treatment should be considered to prevent complications associated with disseminated intravascular coagulation.},
}
@article {pmid39238368,
year = {2024},
author = {Hansen, AK and Argondona, JA and Miao, S and Percy, DM and Degnan, PH},
title = {Rapid loss of nutritional symbionts in an endemic Hawaiian herbivore radiation is associated with plant galling habit.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msae190},
pmid = {39238368},
issn = {1537-1719},
abstract = {Insect herbivores frequently co-speciate with symbionts that enable them to survive on nutritionally unbalanced diets. While ancient symbiont gain and loss events have been pivotal for insect diversification and feeding niche specialization, evidence of recent events is scarce. We examine the recent loss of nutritional symbionts (in as little as 1 MY) in sap-feeding Pariaconus, an endemic Hawaiian insect genus that has undergone adaptive radiation, evolving various galling and free-living ecologies on a single host plant species, Metrosideros polymorpha within the last ∼5MY. Using 16S rRNA sequencing we investigated the bacterial microbiomes of 19 Pariaconus species and identified distinct symbiont profiles associated with specific host-plant ecologies. Phylogenetic analyses and metagenomic reconstructions revealed significant differences in microbial diversity and functions among psyllids with different host-plant ecologies. Within a few MY, Pariaconus species convergently evolved the closed-gall habit twice. This shift to enclosed galls coincided with loss of the Morganella-like symbiont that provides the essential amino acid arginine to free-living and open-gall sister species. After the Pariaconus lineage left Kauai and colonized younger islands, both open- and closed-gall species lost the Dickeya-like symbiont. This symbiont is crucial for synthesizing essential amino acids (phenylalanine, tyrosine, lysine) as well as B-vitamins in free-living species. The recurrent loss of these symbionts in galling species reinforces evidence that galls are nutrient sinks and combined with the rapidity of the evolutionary timeline, highlights the dynamic role of insect-symbiont relationships during the diversification of feeding ecologies. We propose new Candidatus names for the novel Morganella-like and Dickeya-like symbionts.},
}
@article {pmid39237540,
year = {2024},
author = {Ravikrishnan, A and Wijaya, I and Png, E and Chng, KR and Ho, EXP and Ng, AHQ and Mohamed Naim, AN and Gounot, JS and Guan, SP and Hanqing, JL and Guan, L and Li, C and Koh, JY and de Sessions, PF and Koh, WP and Feng, L and Ng, TP and Larbi, A and Maier, AB and Kennedy, BK and Nagarajan, N},
title = {Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {7751},
pmid = {39237540},
issn = {2041-1723},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Singapore ; Male ; Aged, 80 and over ; Female ; *Aging ; *Metagenome ; Asian People/genetics ; Phenotype ; Metagenomics/methods ; Bacteria/genetics/classification/metabolism/isolation &amp; purification ; Bacteroides/genetics/metabolism ; Cohort Studies ; Feces/microbiology ; },
abstract = {While rapid demographic changes in Asia are driving the incidence of chronic aging-related diseases, the limited availability of high-quality in vivo data hampers our ability to understand complex multi-factorial contributions, including gut microbial, to healthy aging. Leveraging a well-phenotyped cohort of community-living octogenarians in Singapore, we used deep shotgun-metagenomic sequencing for high-resolution taxonomic and functional characterization of their gut microbiomes (n = 234). Joint species-level analysis with other Asian cohorts identified distinct age-associated shifts characterized by reduction in microbial richness, and specific Alistipes and Bacteroides species enrichment (e.g., Alistipes shahii and Bacteroides xylanisolvens). Functional analysis confirmed these changes correspond to metabolic potential expansion in aging towards alternate pathways synthesizing and utilizing amino-acid precursors, vis-à-vis dominant microbial guilds producing butyrate in gut from pyruvate (e.g., Faecalibacterium prausnitzii, Roseburia inulinivorans). Extending these observations to key clinical markers helped identify >10 robust microbial associations to inflammation, cardiometabolic and liver health, including potential probiotic species (e.g., Parabacteroides goldsteinii) and pathobionts (e.g., Klebsiella pneumoniae), highlighting the microbiome's role as biomarkers and potential targets for promoting healthy aging.},
}
@article {pmid39237364,
year = {2024},
author = {Chae, JB and Shin, SU and Kim, S and Chae, H and Kim, WG and Chae, JS and Song, H and Kang, JW},
title = {Identification of a new bovine picornavirus (Boosepivirus) in the Republic of Korea.},
journal = {Journal of veterinary science},
volume = {},
number = {},
pages = {},
doi = {10.4142/jvs.24148},
pmid = {39237364},
issn = {1976-555X},
support = {122061-2/IPET/Korea Institute of Planning and Evaluation for Technology in Food, Agriculture and Forestry/Korea ; },
abstract = {IMPORTANCE: Despite advancements in herd management, feeding, and pharmaceutical interventions, neonatal calf diarrhea (NCD) remains a major global health concern. Bacteria, viruses, and parasites are the major contributors to NCD. Although several pathogens have been identified in the Republic of Korea (ROK), the etiological agents of numerous NCD cases have not been identified.<br><br>OBJECTIVES: To identify, for the first time, the prevalence and impact of Boosepivirus (BooV) on calf diarrhea in the ROK.<br><br>METHODS: Here, the unknown cause of calf diarrhea was determined using metagenomics We then explored the prevalence of certain pathogens, including BooV, that cause NCD. Seventy diarrheal fecal samples from Hanwoo (Bos taurus coreanae) calves were analyzed using reverse transcriptase and quantitative real-time polymerase chain reaction for pathogen detection and BooV isolate sequencing.<br><br>RESULTS: The complete genome of BooV was detected from unknown causes of calf diarrhea. And also, BooV was the most frequently detected pathogen (35.7%) among 8 pathogens in 70 diarrheic feces from Hanwoo calves. Co-infection analyses indicated that most BooV-positive samples were solely infected with BooV, indicating its significance in NCD in the ROK. All isolates were classified as BooV B in phylogenetic analysis.<br><br>CONCLUSIONS AND RELEVANCE: This is the first study to determine the prevalence and molecular characteristics of BooV in calf diarrhea in the ROK, highlighting the potential importance of BooV as a causative agent of calf diarrhea and highlighting the need for further research on its epidemiology and pathogenicity.},
}
@article {pmid39236909,
year = {2024},
author = {Chen, H and Tang, M and He, L and Xiao, X and Yang, F and He, Q and Sun, S and Gao, Y and Zhou, L and Li, Y and Sun, J and Zhang, W},
title = {Exploring the impact of fulvic acid on electrochemical hydrogen-driven autotrophic denitrification system: Performance, microbial characteristics and mechanism.},
journal = {Bioresource technology},
volume = {412},
number = {},
pages = {131432},
doi = {10.1016/j.biortech.2024.131432},
pmid = {39236909},
issn = {1873-2976},
mesh = {*Denitrification ; *Autotrophic Processes ; *Benzopyrans ; *Hydrogen/metabolism ; Nitrates/metabolism ; Nitrogen ; Bacteria/metabolism ; Electrochemical Techniques/methods ; },
abstract = {In this study, the effect of modulating fulvic acid (FA) concentrations (0, 25 and 50 mg/L) on nitrogen removal in a bioelectrochemical hydrogen autotrophic denitrification system (BHDS) was investigated. Results showed that FA increased the nitrate (NO3[-]-N) removal rate of the BHDSs from 37.8 to 46.2 and 45.2 mg N/(L·d) with a current intensity of 40 mA. The metagenomic analysis revealed that R2 (25 mg/L) was predominantly populated by autotrophic denitrifying microorganisms, which enhanced denitrification performance by facilitating electron transfer. Conversely, R3 (50 mg/L) exhibited an increase in genes related to the heterotrophic process, which improved the denitrification performance through the collaborative action of both autotrophic and heterotrophic denitrification pathways. Besides, the study also identified a potential for nitrogen removal in Serpentinimonas, which have been rarely studied. The interesting set of findings provide valuable reference for optimizing BHDS for nitrogen removal and promoting specific denitrifying genera within the system.},
}
@article {pmid39236908,
year = {2024},
author = {Cui, P and Wan, N and Li, C and Zou, L and Ma, M and Du, J and Jiang, Y},
title = {Comparative analysis of sulfur-driven autotrophic denitrification for pilot-scale application: Pollutant removal performance and metagenomic function.},
journal = {Bioresource technology},
volume = {413},
number = {},
pages = {131433},
doi = {10.1016/j.biortech.2024.131433},
pmid = {39236908},
issn = {1873-2976},
abstract = {Two parallel pilot-scale reactors were operated to investigate pollutant removal performance and metabolic pathways in elemental sulfur-driven autotrophic denitrification (SDAD) process under low temperature and after addition of external electron donors. The results showed that low temperature slightly inhibited SDAD (average total nitrogen removal of ∼4.7 mg L[-1]) while supplement of sodium thiosulfate (stage 2) and sodium acetate (stage 3) enhanced denitrification and secretion of extracellular polymeric substances (EPS), leading to the average removal rate of 0.75 and 1.01 kg N m[-3] d[-1], respectively with over twice higher total EPS. Correspondingly, nitrogen and sulfur related microbial metabolisms especially nitrite reductase and nitric oxide reductase encoding were promoted by genera including Thermomonas and Thiobacillus. The variations revealed that extra sodium acetate improved denitrification and enriched more SDAD-related microorganisms compared with sodium thiosulfate, which potentially catalyzed the refinement of practical strategies for optimizing denitrification in low carbon to nitrogen ratio wastewater treatment.},
}
@article {pmid39236827,
year = {2024},
author = {Xu, W and Xu, Y and Sun, R and Rey Redondo, E and Leung, KK and Wan, SH and Li, J and Yung, CCM},
title = {Revealing the intricate temporal dynamics and adaptive responses of prokaryotic and eukaryotic microbes in the coastal South China Sea.},
journal = {The Science of the total environment},
volume = {952},
number = {},
pages = {176019},
doi = {10.1016/j.scitotenv.2024.176019},
pmid = {39236827},
issn = {1879-1026},
mesh = {China ; *Phytoplankton/physiology/genetics ; *Seawater/microbiology ; Microbiota ; Cyanobacteria/genetics/physiology ; Photosynthesis ; Seasons ; Metagenome ; },
abstract = {This comprehensive two-year investigation in the coastal South China Sea has advanced our understanding of marine microbes at both community and genomic levels. By combining metagenomics and metatranscriptomics, we have revealed the intricate temporal dynamics and remarkable adaptability of microbial communities and phytoplankton metagenome-assembled genomes (MAGs) in response to environmental fluctuations. We observed distinct seasonal shifts in microbial community composition and function: cyanobacteria were predominant during warmer months, whereas photosynthetic protists were more abundant during colder seasons. Notably, metabolic marker KOs of photosynthesis were consistently active throughout the year, underscoring the persistent role of these processes irrespective of seasonal changes. Our analysis reveals that environmental parameters such as temperature, salinity, and nitrate concentrations profoundly influence microbial community composition, while temperature and silicate have emerged as crucial factors shaping their functional traits. Through the recovery and analysis of 37 phytoplankton MAGs, encompassing nine prokaryotic cyanobacteria and 28 eukaryotic protists from diverse phyla, we have gained insights into their genetic diversity and metabolic capabilities. Distinct profiles of photosynthesis-related pathways including carbon fixation, carotenoid biosynthesis, photosynthesis-antenna proteins, and photosynthesis among the MAGs indicated their genetic adaptations to changing environmental conditions. This study not only enhances our understanding of microbial dynamics in coastal marine ecosystems but also sheds light on the ecological roles and adaptive responses of different microbial groups to environmental changes.},
}
@article {pmid39236545,
year = {2024},
author = {Wang, R and Wang, Z and Yuan, H and Li, C and Zhu, N},
title = {Mechanistic exploration of COVlD-19 antiviral drug ritonavir on anaerobic digestion through experimental validation coupled with metagenomics analysis.},
journal = {Journal of hazardous materials},
volume = {479},
number = {},
pages = {135603},
doi = {10.1016/j.jhazmat.2024.135603},
pmid = {39236545},
issn = {1873-3336},
mesh = {Anaerobiosis ; *Antiviral Agents/pharmacology ; *Metagenomics ; *Ritonavir ; *Sewage/microbiology ; *Methane/metabolism ; COVID-19 Drug Treatment ; Bioreactors ; },
abstract = {Aggregation of antiviral drugs (ATVs) in waste activated sludge (WAS) poses considerable environmental risk, so it is crucial to understand the behavior of these agents during WAS treatment. This study investigated the effects of ritonavir (RIT), an ATV used to treat human immunodeficiency virus infection and coronavirus disease 2019, on anaerobic digestion (AD) of WAS to reveal the mechanisms by which it interferes with anaerobic flora. The dosage influence results showed that methane production in AD of WAS decreased by 46.56 % when RIT concentration was increased to 1000 μg/kg total suspended solids (TSS). The AD staging test revealed that RIT mainly stimulated microbial synthesis of the extracellular polymeric substance (EPS), limiting organic matter solubilization. At 500 μg/kg TSS, RIT decreased CHO and CHON levels in dissolved organic matter by 23.12 % and 56.68 %, respectively, significantly reducing substrate availability to microorganisms. Metagenomic analysis of microbial functional gene sets revealed that RIT had greater inhibitory effects on protein and amino acid metabolism than on carbohydrate metabolism. Under RIT stress, methanogens switched from hydrogenotrophic and acetotrophic methanogenesis to methylotrophic and acetotrophic methanogenesis.},
}
@article {pmid39236503,
year = {2024},
author = {Wang, D and Meng, Y and Huang, LN and Zhang, XX and Luo, X and Meng, F},
title = {A comprehensive catalog encompassing 1376 species-level genomes reveals the core community and functional diversity of anammox microbiota.},
journal = {Water research},
volume = {266},
number = {},
pages = {122356},
doi = {10.1016/j.watres.2024.122356},
pmid = {39236503},
issn = {1879-2448},
abstract = {Research on the microbial community and function of the anammox process for environmentally friendly wastewater treatment has achieved certain success, which may mean more universal insights are needed. However, the comprehensive understanding of the anammox process is constrained by the limited taxonomic assignment and functional characterization of anammox microbiota, primarily due to the scarcity of high-quality genomes for most organisms. This study reported a global genome catalog of anammox microbiotas based on numerous metagenomes obtained from both lab- and full-scale systems. A total of 1376 candidate species from 7474 metagenome-assembled genomes were used to construct the genome catalog, providing extensive microbial coverage (averaged of 92.40 %) of anammox microbiota. Moreover, a total of 64 core genera and 44 core species were identified, accounting for approximately 64.25 % and 43.97 %, respectively, of anammox microbiota. The strict core genera encompassed not only functional bacteria (e.g., Brocadia, Desulfobacillus, Zeimonas, and Nitrosomonas) but also two candidate genera (UBA12294 and OLB14) affiliated with the order Anaerolineales. In particular, core denitrifying bacteria with observably taxonomic diversity exhibited diverse functional profiles; for instance, the potential of carbohydrate metabolism in Desulfobacillus and Zeimonas likely improves the mixotrophic lifestyle of anammox microbiota. Besides, a noteworthy association was detected between anammox microbiota and system type. Microbiota in coupling system exhibited complex diversity and interspecies interactions by limiting numerous core denitrifying bacteria. In summary, the constructed catalog substantially expands our understanding of the core community and their functions of anammox microbiota, providing a valuable resource for future studies on anammox systems.},
}
@article {pmid39235833,
year = {2024},
author = {Hsouna, J and Gritli, T and Ilahi, H and Han, JC and Ellouze, W and Zhang, XX and Mansouri, M and Rahi, P and El Idrissi, MM and Lamrabet, M and Courty, PE and Wipf, D and Bekki, A and Tambong, JT and Mnasri, B},
title = {Rhizobium aouanii sp. nov., efficient nodulating rhizobia isolated from Acacia saligna roots in Tunisia.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {74},
number = {9},
pages = {},
pmid = {39235833},
issn = {1466-5034},
mesh = {*Phylogeny ; *Rhizobium/genetics/classification/isolation &amp; purification ; *DNA, Bacterial/genetics ; *Acacia/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Sequence Analysis, DNA ; *Bacterial Typing Techniques ; *Fatty Acids/analysis ; Tunisia ; *Nucleic Acid Hybridization ; *Root Nodules, Plant/microbiology ; Genes, Essential/genetics ; Genes, Bacterial ; Base Composition ; Symbiosis ; },
abstract = {Three bacterial strains, 1AS14I[T], 1AS12I and 6AS6, isolated from root nodules of Acacia saligna, were characterized using a polyphasic approach. Phylogenetic analysis based on rrs sequences placed all three strains within the Rhizobium leguminosarum complex. Further phylogeny, based on 1 756 bp sequences of four concatenated housekeeping genes (recA, atpD, glnII and gyrB), revealed their distinction from known rhizobia species of the R. leguminosarum complex (Rlc), forming a distinct clade. The closest related species, identified as Rhizobium laguerreae, with a sequence identity of 96.4% based on concatenated recA-atpD-glnII-gyrB sequences. The type strain, 1AS14I[T], showed average nucleotide identity (ANI) values of 94.9, 94.3 and 94.1% and DNA-DNA hybridization values of 56.1, 57.4 and 60.0% with the type strains of closest known species: R. laguerreae, Rhizobium acaciae and 'Rhizobium indicum', respectively. Phylogenomic analyses using 81 up-to-date bacteria core genes and the Type (Strain) Genome Server pipeline further supported the uniqueness of strains 1AS14I[T], 1AS12I and 6AS6. The relatedness of the novel strains to NCBI unclassified Rhizobium sp. (396 genomes) and metagenome-derived genomes showed ANI values from 76.7 to 94.8% with a species-level cut-off of 96%, suggesting that strains 1AS14I, 1AS12I and 6AS6 are a distinct lineage. Additionally, differentiation of strains 1AS14I[T], 1AS12I and 6AS6 from their closest phylogenetic neighbours was achieved using phenotypic, physiological and fatty acid content analyses. Based on the genomic, phenotypic and biochemical data, we propose the establishment of a novel rhizobial species, Rhizobium aouanii sp. nov., with strain 1AS14I[T] designated as the type strain (=DSM 113914[T]=LMG 33206[T]). This study contributes to the understanding of microbial diversity in nitrogen-fixing symbioses, specifically within Acacia saligna ecosystems in Tunisia.},
}
@article {pmid39235751,
year = {2025},
author = {Lemée, P and Bridier, A},
title = {Bioinformatic Pipeline for Profiling Foodborne Bacterial Ecology and Resistome from Short-Read Metagenomics.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2852},
number = {},
pages = {289-309},
pmid = {39235751},
issn = {1940-6029},
mesh = {*Metagenomics/methods ; *Computational Biology/methods ; *Food Microbiology/methods ; *Bacteria/genetics ; *High-Throughput Nucleotide Sequencing/methods ; Metagenome ; Microbiota/genetics ; },
abstract = {Next-generation sequencing revolutionized food safety management these last years providing access to a huge quantity of valuable data to identify, characterize, and monitor bacterial pathogens on the food chain. Shotgun metagenomics emerged as a particularly promising approach as it enables in-depth taxonomic profiling and functional investigation of food microbial communities. In this chapter, we provide a comprehensive step-by-step bioinformatical workflow to characterize bacterial ecology and resistome composition from metagenomic short-reads obtained by shotgun sequencing.},
}
@article {pmid39235268,
year = {2024},
author = {Sudarshan, AS and Dai, Z and Gabrielli, M and Oosthuizen-Vosloo, S and Konstantinidis, KT and Pinto, AJ},
title = {New Drinking Water Genome Catalog Identifies a Globally Distributed Bacterial Genus Adapted to Disinfected Drinking Water Systems.},
journal = {Environmental science &amp; technology},
volume = {58},
number = {37},
pages = {16475-16487},
pmid = {39235268},
issn = {1520-5851},
mesh = {*Drinking Water/microbiology ; Disinfection ; Bacteria/genetics ; Microbiota ; Genome, Bacterial ; Metagenome ; },
abstract = {Genome-resolved insights into the structure and function of the drinking water microbiome can advance the effective management of drinking water quality. To enable this, we constructed and curated thousands of metagenome-assembled and isolate genomes from drinking water distribution systems globally to develop a Drinking Water Genome Catalog (DWGC). The current DWGC disproportionately represents disinfected drinking water systems due to a paucity of metagenomes from nondisinfected systems. Using the DWGC, we identify core genera of the drinking water microbiome including a genus (UBA4765) within the order Rhizobiales that is frequently detected and highly abundant in disinfected drinking water systems. We demonstrate that this genus has been widely detected but incorrectly classified in previous amplicon sequencing-based investigations of the drinking water microbiome. Further, we show that a single genome variant (genomovar) within this genus is detected in 75% of drinking water systems included in this study. We propose a name for this uncultured bacterium as "Raskinella chloraquaticus" and describe the genus as "Raskinella" (endorsed by SeqCode). Metabolic annotation and modeling-based predictions indicate that this bacterium is capable of necrotrophic growth, is able to metabolize halogenated compounds, proliferates in a biofilm-based environment, and shows clear indications of disinfection-mediated selection.},
}
@article {pmid39235252,
year = {2024},
author = {Sweet, P and Burroughs, M and Jang, S and Contreras, L},
title = {TolRad, a model for predicting radiation tolerance using Pfam annotations, identifies novel radiosensitive bacterial species from reference genomes and MAGs.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0383823},
doi = {10.1128/spectrum.03838-23},
pmid = {39235252},
issn = {2165-0497},
abstract = {UNLABELLED: The trait of ionizing radiation (IR) tolerance is variable between bacterium, with species succumbing to acute doses as low as 60 Gy and extremophiles able to survive doses exceeding 10,000 Gy. While survival screens have identified multiple highly radioresistant bacteria, such systemic searches have not been conducted for IR-sensitive bacteria. The taxonomy-level diversity of IR sensitivity is poorly understood, as are genetic elements that influence IR sensitivity. Using the protein domain (Pfam) frequencies from 61 bacterial species with experimentally determined D10 values (the dose at which only 10% of the population survives), we trained TolRad, a random forest binary classifier, to distinguish between radiosensitive (D10 < 200 Gy) and radiation-tolerant (D10 > 200 Gy) bacteria. On untrained species, TolRad had an accuracy of 0.900. We applied TolRad to 152 UniProt-hosted bacterial proteomes associated with the human microbiome, including 37 strains from the ATCC Human Microbiome Collection, and classified 34 species as radiosensitive. Whereas IR-sensitive species (D10 < 200 Gy) in the training data set had been confined to the phylum Proteobacterium, this initial TolRad screen identified radiosensitive bacteria in two additional phyla. We experimentally validated the predicted radiosensitivity of a Bacteroidota species from the human microbiome. To demonstrate that TolRad can be applied to metagenome-assembled genomes (MAGs), we tested the accuracy of TolRad on Egg-NOG assembled proteomes (0.965) and partial proteomes. Finally, three collections of MAGs were screened using TolRad, identifying further phyla with radiosensitive species and suggesting that environmental conditions influence the abundance of radiosensitive bacteria.<br><br>IMPORTANCE: Bacterial species have vast genetic diversity, allowing for life in extreme environments and the conduction of complex chemistry. The ability to harness the full potential of bacterial diversity is hampered by the lack of high-throughput experimental or bioinformatic methods for characterizing bacterial traits. Here, we present a computational model that uses de novo-generated genome annotations to classify a bacterium as tolerant of ionizing radiation (IR) or as radiosensitive. This model allows for rapid screening of bacterial communities for low-tolerance species that are of interest for both mechanistic studies into bacterial sensitivity to IR and biomarkers of IR exposure.},
}
@article {pmid39235142,
year = {2024},
author = {Zhao, HX and He, H and Zeng, C and Zhang, TY and Hu, CY and Pan, R and Xu, MY and Tang, YL and Xu, B},
title = {Overlooked Role of Fungi in Drinking Water Taste and Odor Issues.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c02575},
pmid = {39235142},
issn = {1520-5851},
abstract = {Taste and odor (T&amp;O) are among the most frequently encountered aesthetic issues in drinking water. While fungi have been reported to produce offensive odors, their contribution to T&amp;O in drinking water remains understudied and often overlooked. In this study, the profiles of fungal community and odorants produced by 10 native fungal isolates were investigated in 36 samples collected from two drinking water treatment plants and a premise plumbing system. A total of 17 odorants were identified with Penicillium, Aspergillus, Paecilomyces, and Alternaria genera exhibiting the highest odorant yields. Significant concentrations of musty/earthy compounds were produced by these fungal isolates, such as 2-methylisoborneol (2-MIB) (26-256 ng/L), geosmin (10-13 ng/L), and 2-isobutyl-3-methoxy-pyrazine (IBMP) (3-13 ng/L). The high odor activity value of the odorants primarily occurred within 4 d, while toxicity continued to increase during the 8 d incubation. UV treatment in premise plumbing significantly (p < 0.05) reduced the gene read counts of Ascomycota phylum, Aspergillus spp., Fusarium spp., Rhizopus spp., and Trichoderma spp., by 2.3-4.0 times. These findings underscore the previously underestimated role of fungi in contributing to T&amp;O issues in drinking water and corresponding risks to consumers and indicate UV as a promising strategy for fungal control in drinking water.},
}
@article {pmid39235032,
year = {2024},
author = {Zhou, Y and Cheng, SL and Fang, HJ and Yang, Y and Guo, YF and Li, YN and Shi, FY and Wang, H and Chen, L},
title = {[Research advances in the response of soil nitrogen emissions from peatlands to climate warming and drying].},
journal = {Ying yong sheng tai xue bao = The journal of applied ecology},
volume = {35},
number = {6},
pages = {1725-1734},
doi = {10.13287/j.1001-9332.202406.030},
pmid = {39235032},
issn = {1001-9332},
mesh = {*Soil/chemistry ; *Nitrogen/analysis/metabolism ; *Climate Change ; *Global Warming ; *Soil Microbiology ; Ecosystem ; Droughts ; Nitrous Oxide/analysis/metabolism ; },
abstract = {Climate warming and drying has led to a sharp increase in nitrogen (N) emissions from the boreal peatland soils, but the underlying microbial-mediated mechanism is still unclear. We reviewed the responses of soil N transformation and emission in alpine peatland to temperature increases and water table changes, the interaction between soil anaerobic ammonia oxidation (Anammox) and NO3[-] dissimilatory reduction processes, and soil N2O production pathways and their contributions. There are several knowledge gaps. First, the amount of N loss in peatlands in alpine areas is seriously underestimated because most studies focused only on soil N2O emissions and ignored the release of N2. Second, the contribution of Anammox process to N2 emissions from peatlands is not quantified. Third, there is a lack of quantification of the relative contributions of Anammox, bacterial denitrification, and fungal co-denitrification processes to N2 loss. Finally, the decoupling mechanism of Anammox and NO3[-] reduction processes under a warming and drying climate scenario is not clear. Considering aforementioned shortages in previous studies, we proposed the directions and contents for future research. Through building an experimental platform with field warming and water level controlling, combining stable isotope, molecular biology, and metagenomics technology, the magnitude, composition ratio and main controlling factors of N emissions (N2O, NO, and N2) in boreal peatlands should be systematically investigated. The interaction among the main N loss processes in soils as well as the relative contributions of nitrification, anaerobic ammonia oxidation, and denitrification to N2O and N2 productions should be investigated and quantified. Furthermore, the sensitive microbial groups and the coupling between soil N transformations and microbial community succession should be clarified to reveal the microbiological mechanism underlying the responses of soil N turnover process to climate warming and drying.},
}
@article {pmid39234039,
year = {2024},
author = {Wang, L and Zhang, W and Dai, S and Gao, Y and Zhu, C and Yu, Y},
title = {Correlation between the gut microbiota characteristics of hosts with severe acute pancreatitis and secondary intra-abdominal infection.},
journal = {Frontiers in medicine},
volume = {11},
number = {},
pages = {1409409},
pmid = {39234039},
issn = {2296-858X},
abstract = {OBJECTIVE: The objective of the study is to investigate the changes in the composition of intestinal microecology in severe acute pancreatitis (SAP) patients with or without intra-abdominal infection and also to analyze the expression of antibiotic resistance genes to provide evidence for early warning of infectious diseases and the rational use of antibiotics.<br><br>METHODS: Twenty patients with SAP were enrolled in the study. According to whether the enrolled patients had a secondary intra-abdominal infection, they were divided into two groups, each consisting of 10 patients. Stool specimens were collected when the patients were admitted to the emergency intensive care unit (EICU), and nucleic acid extraction was performed. Next-generation gene sequencing was used to compare the differences in intestinal microflora diversity and drug resistance gene expression between the two groups.<br><br>RESULTS: The gut microbiota of patients in the infection group exhibited distribution on multiple clustered branches with some intra-group heterogeneity, and their flora diversity was compromised. The infected group showed an enrichment of various opportunistic bacteria in the gut microbiota, along with a high number of metabolic functions, stress functions to external signals, and genes associated with pathogenesis. Drug resistance genes were expressed in the gut microbiota of both groups, but their abundance was significantly lower in the non-infected group.<br><br>CONCLUSION: The intestinal microbiota of patients in the infection group exhibited distribution on multiple clustered branches with some intra-group heterogeneity, and their flora diversity was compromised. Additionally, drug resistance genes were expressed in the gut microbiota of both groups, although their abundance was significantly lower in the non-infected group.},
}
@article {pmid39233907,
year = {2024},
author = {Yuan, J and Wang, L and Zhang, W and Deng, C and Li, Q and Meng, Y and Chen, Y},
title = {Performance of metagenomic Next-Generation Sequencing and metagenomic Nanopore Sequencing for the diagnosis of tuberculosis in HIV-positive patients.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1423541},
pmid = {39233907},
issn = {2235-2988},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; Male ; *Tuberculosis/diagnosis/microbiology ; Female ; *HIV Infections/complications ; *Mycobacterium tuberculosis/genetics/isolation &amp; purification ; Retrospective Studies ; Adult ; *Sensitivity and Specificity ; Middle Aged ; *Coinfection/diagnosis/microbiology/virology ; *Nanopore Sequencing/methods ; *Metagenomics/methods ; },
abstract = {BACKGROUND: Patients who were infected by the Human Immunodeficiency Virus (HIV) could have weakened immunity that is complicated by opportunistic infections, especially for Mycobacterium tuberculosis (MTB). Notably, the HIV-MTB co-infection will accelerate the course of disease progress and greatly increase the mortality of patients. Since the traditional diagnostic methods are time-consuming and have low sensitivity, we aim to investigate the performance of mNGS (metagenomic Next-Generation Sequencing) and mNPS (metagenomic NanoPore Sequencing) for the rapid diagnosis of tuberculosis in HIV-infected patients.<br><br>METHODS: The 122 HIV-infected patients were enrolled for the retrospective analysis. All of the patients underwent traditional microbiological tests, mNGS, and (or) mNPS tests. The clinical comprehensive diagnosis was used as the reference standard to compare the diagnostic performance of culture, mNGS, and mNPS on tuberculosis. We also investigate the diagnostic value of mNGS and mNPS on mixed-infection. Furthermore, the treatment adjustment directed by mNGS and mNPS was analyzed.<br><br>RESULTS: Compared with the composite reference standard, the culture showed 42.6% clinical sensitivity and 100% specificity, and the OMT(other microbiological testing) had 38.9% sensitivity and 100% specificity. The mNGS had 58.6% clinical sensitivity and 96.8% specificity, and the mNPS had 68.0% clinical sensitivity and 100% specificity. The proportion of mixed-infection cases (88.9%) in the TB group was higher than those in the non-TB group (54.8%) and the mNGS and mNPS are more competitive on mixed-infection diagnosis compared with the traditional methods. Furthermore, there are 63 patients (69.2%) and 36 patients (63.2%) achieved effective treatment after receiving the detection of mNPS and mNGS, respectively.<br><br>CONCLUSION: Our study indicated that mNPS and mNGS have high sensitivity and specificity for TB diagnosis compared with the traditional methods, and mNPS seems to have better diagnostic performance than mNGS. Moreover, mNGS and mNPS showed apparent advantages in detecting mixed infection. The mNPS and mNGS-directed medication adjustment have effective treatment outcomes for HIV-infected patients who have lower immunity.},
}
@article {pmid39233549,
year = {2024},
author = {Yin, C and Cong, Y and Wang, H and Wang, D and Yang, X and Wang, X and Wang, T},
title = {Pathogenic Detection by Metagenomic next-generation Sequencing in Spinal Infections.},
journal = {Spine},
volume = {},
number = {},
pages = {},
doi = {10.1097/BRS.0000000000005148},
pmid = {39233549},
issn = {1528-1159},
abstract = {STUDY DESIGN: Retrospective, observational study.<br><br>OBJECTIVE: To evaluate the ability and value of metagenomic next-generation sequencing (mNGS) in detecting pathogens from spinal infections.<br><br>BACKGROUND: The pathogenic diagnosis of primary spinal infection is challenging. The widespread application of mNGs in clinical practice makes it particularly useful in detecting rare, emerging, and atypical complex infectious diseases.<br><br>METHODS: From January 2019 to December 2023, a retrospective collection of 120 samples was obtained from patients suspected of spinal infections and undergoing treatment. Pairwise comparisons between traditional laboratory tests and mNGS were conducted for all cases.<br><br>RESULTS: Among the 120 cases, 95 were diagnosed as spinal infections, while 25 were classified as non-infectious. Microbiological evidence was found in 59 cases, while 36 cases were clinically diagnosed as spinal infection without definitive microbiological evidence. Rare microorganisms such as Aspergillus fumigatus, Taifanglania major, and Coxiella burnetii were detected by mNGS. The positive rate of mNGS was significantly higher at 88.42% compared to microbiological culture (43.16%), P<0.001. At the genus level, mNGS exhibited a consistency rate of 86.44% (51/59) with confirmed microorganisms. MNGS demonstrated very good agreement with clinically confirmed microorganisms at the genus level (kappa=0.833). The sensitivity, specificity, positive predictive value, and negative predictive value of mNGS were 86.44%, 92.00%, 96.23%, and 74.19%, respectively.<br><br>CONCLUSIONS: The mNGS test exhibits rapidity, efficiency, and accuracy, rendering it of immense diagnostic and therapeutic value in the realm of spinal infection diseases.},
}
@article {pmid39233185,
year = {2024},
author = {Huang, J and Wang, C and Huang, X and Zhang, Q and Feng, R and Wang, X and Zhang, S and Wang, J},
title = {Long-term effect of phenol, quinoline, and pyridine on nitrite accumulation in the nitrification process: performance, microbial community, metagenomics and molecular docking analysis.},
journal = {Bioresource technology},
volume = {412},
number = {},
pages = {131407},
doi = {10.1016/j.biortech.2024.131407},
pmid = {39233185},
issn = {1873-2976},
mesh = {*Molecular Docking Simulation ; *Nitrification ; *Nitrites/metabolism ; *Quinolines/pharmacology ; *Metagenomics/methods ; *Pyridines/pharmacology/metabolism ; Phenol ; Bacteria/metabolism/drug effects ; Microbiota/drug effects ; Wastewater ; Oxidoreductases/metabolism ; Ammonia/metabolism ; },
abstract = {Phenol, quinoline, and pyridine, commonly found in industrial wastewater, disrupt the nitrification process, leading to nitrite accumulation. This study explores the potential mechanisms through which these biotoxic organic compounds affect nitrite accumulation, using metagenomic and molecular docking analyses. Despite increasing concentrations of these compounds from 40 to 160 mg/L, ammonia nitrogen removal was not hindered, and stable nitrite accumulation rates exceeding 90 % were maintained. Additionally, these compounds inhibited nitrite-oxidizing bacteria (NOB) and enriched ammonia-oxidizing bacteria (AOB) in situ. As the concentration of these compounds rose, protein (PN) and polysaccharide (PS) concentrations also increased, along with a higher PN/PS ratio. Metagenomic analysis further revealed an increase in hao relative abundance, while microbial community analysis showed increased Nitrosomonas abundance, which contributed to nitrite accumulation stability. Molecular docking indicated that these compounds have lower binding energy with hydroxylamine oxidoreductase (HAO) and nitrate reductase (NAR), theoretically supporting the observed sustained nitrite accumulation.},
}
@article {pmid39233139,
year = {2024},
author = {Chawla, K and Shaji, R and Siddalingaiah, N and P K, SM and M D, S and Lewis, LES and Nagaraja, SB},
title = {Next generation sequencing to detect pathogens causing paediatric community-acquired pneumonia - A systematic review and meta-analysis.},
journal = {Indian journal of medical microbiology},
volume = {52},
number = {},
pages = {100730},
doi = {10.1016/j.ijmmb.2024.100730},
pmid = {39233139},
issn = {1998-3646},
abstract = {BACKGROUND: Paediatric community-acquired pneumonia (CAP) is a major public health challenge in children, requiring accurate and timely diagnosis of causative pathogens for effective antibiotic treatment. We aimed to explore the utility of next-generation sequencing (NGS) in precise diagnosis of pediatric CAP and its effect on treatment outcome of these children.<br><br>METHODS: A systematic review and meta-analysis was conducted to compare NGS-guided antibiotic therapy with conventional methods in pediatric CAP. The study followed PRISMA guidelines and searched for electronic databases including PubMed/MEDLINE, Embase, Scopus, and Web of Sciences from 2012 to 2023. Studies on pediatric CAP (<18 years) using NGS alongside conventional diagnostics, were included.<br><br>RESULTS: Database search identified 721 studies and 6 were finally included for review, published between 2019 and 2023. Meta-analysis revealed an overall odds ratio of 2.39 (95&#xa0;% CI 1.22, 3.56) for NGS vs conventional methods. Detection rates using NGS ranged from 86% to 100&#xa0;%, surpassing conventional methods (26%-78.51&#xa0;%). Five out of selected 6 studies (83.33&#xa0;%) have documented that change in treatment based on NGS finding resulted in clinical improvement of patients. There was no significant heterogeneity and potential bias among the studies. Nearly 80&#xa0;% of the studies were of good quality.<br><br>CONCLUSION: The NGS (particularly metagenomic sequencing) is a promising tool for diagnosing paediatric CAP with high accuracy. It can improve antibiotic usage practices and patient outcomes, potentially reducing antibiotic resistance. Based on meta-analysis, training of healthcare professionals in NGS methodologies and result interpretation is highly recommended.},
}
@article {pmid39232827,
year = {2024},
author = {Sun, C and Hu, G and Yi, L and Ge, W and Yang, Q and Yang, X and He, Y and Liu, Z and Chen, WH},
title = {Integrated analysis of facial microbiome and skin physio-optical properties unveils cutotype-dependent aging effects.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {163},
pmid = {39232827},
issn = {2049-2618},
support = {2019YFA0905600//National Key Research and Development Program of China/ ; },
mesh = {Humans ; *Microbiota ; *Skin/microbiology ; *Face/microbiology ; Middle Aged ; *Skin Aging/physiology ; Female ; Adult ; Male ; *Bacteria/classification/genetics/isolation &amp; purification ; Aged ; Aging ; Metagenome ; Young Adult ; High-Throughput Nucleotide Sequencing ; Sebum/metabolism ; },
abstract = {BACKGROUND: Our facial skin hosts millions of microorganisms, primarily bacteria, crucial for skin health by maintaining the physical barrier, modulating immune response, and metabolizing bioactive materials. Aging significantly influences the composition and function of the facial microbiome, impacting skin immunity, hydration, and inflammation, highlighting potential avenues for interventions targeting aging-related facial microbes amidst changes in skin physiological properties.<br><br>RESULTS: We conducted a multi-center and deep sequencing survey to investigate the intricate interplay of aging, skin physio-optical conditions, and facial microbiome. Leveraging a newly-generated dataset of 2737 species-level metagenome-assembled genomes (MAGs), our integrative analysis highlighted aging as the primary driver, influencing both facial microbiome composition and key skin characteristics, including moisture, sebum production, gloss, pH, elasticity, and sensitivity. Further mediation analysis revealed that skin characteristics significantly impacted the microbiome, mostly as a mediator of aging. Utilizing this dataset, we uncovered two consistent cutotypes across sampling cities and identified aging-related microbial MAGs. Additionally, a Facial Aging Index (FAI) was formulated based on the microbiome, uncovering the cutotype-dependent effects of unhealthy lifestyles on skin aging. Finally, we distinguished aging related microbial pathways influenced by lifestyles with cutotype-dependent effect.<br><br>CONCLUSIONS: Together, our findings emphasize aging's central role in facial microbiome dynamics, and support personalized skin microbiome interventions by targeting lifestyle, skin properties, and aging-related microbial factors. Video Abstract.},
}
@article {pmid39232674,
year = {2024},
author = {Pan, TJ and Luo, WW and Zhang, SS and Xie, JY and Xu, Z and Zhong, YY and Zou, XF and Gong, HJ and Ye, ML},
title = {The clinical application value of multi-site mNGS detection of patients with sepsis in intensive care units.},
journal = {BMC infectious diseases},
volume = {24},
number = {1},
pages = {920},
pmid = {39232674},
issn = {1471-2334},
mesh = {Humans ; *Sepsis/diagnosis/microbiology ; *Intensive Care Units ; Male ; Female ; Middle Aged ; Retrospective Studies ; Aged ; *High-Throughput Nucleotide Sequencing ; *Metagenomics/methods ; Adult ; Bacteria/isolation &amp; purification/genetics/classification ; Aged, 80 and over ; },
abstract = {BACKGROUND: Sepsis remains a leading cause of mortality in intensive care units, and rapid and accurate pathogen detection is crucial for effective treatment. This study evaluated the clinical application of multi-site metagenomic next-generation sequencing (mNGS) for the diagnosis of sepsis, comparing its performance against conventional methods.<br><br>METHODS: A retrospective analysis was conducted on 69 patients with sepsis consecutively admitted to the Department of Intensive Care Medicine, Meizhou People's Hospital. Samples of peripheral blood and infection sites were collected for mNGS and conventional method tests to compare the positive rate of mNGS and traditional pathogen detection methods and the distribution of pathogens. The methods used in this study included a comprehensive analysis of pathogen consistency between peripheral blood and infection site samples. Additionally, the correlation between the pathogens detected and clinical outcomes was investigated.<br><br>RESULTS: Of the patients with sepsis, 57.97% experienced dyspnea, and 65.2% had underlying diseases, with hypertension being the most common. mNGS demonstrated a significantly higher pathogen detection rate (88%) compared to the conventional method tests (26%). The pathogen consistency rate was 60% between plasma and bronchoalveolar lavage fluid samples, and that of plasma and local body fluid samples was 63%. The most frequently detected pathogens were gram-negative bacteria, and Klebsiella pneumonia. There were no significant differences in the clinical features between the pathogens.<br><br>CONCLUSION: mNGS is significantly superior to conventional methods in pathogen detection. There was a notable high pathogen consistency detection between blood and local body fluid samples, supporting the clinical relevance of mNGS. This study highlights the superiority of mNGS in detecting a broad spectrum of pathogens quickly and accurately.<br><br>TRIAL REGISTRATION: Not applicable.},
}
@article {pmid39232327,
year = {2024},
author = {Wang, D and Zhang, J and Han, W and Wu, P and Deng, L and Wang, W},
title = {Ammonia oxidizing bacteria (AOB) denitrification and bacterial denitrification as the main culprit of high N2O emission in SBR with low C/N ratio wastewater.},
journal = {Journal of environmental management},
volume = {369},
number = {},
pages = {122357},
doi = {10.1016/j.jenvman.2024.122357},
pmid = {39232327},
issn = {1095-8630},
mesh = {*Denitrification ; *Wastewater/chemistry ; *Ammonia/metabolism ; *Bacteria/metabolism ; *Nitrous Oxide/metabolism ; *Nitrogen/metabolism ; Carbon/metabolism ; Bioreactors ; Waste Disposal, Fluid/methods ; Oxidation-Reduction ; },
abstract = {A large amount of greenhouse gas nitrous oxide (N2O) will be produced during the biological nitrogen removal process for organic wastewater of low C/N ratio. One of the effective methods to solve this problem is to incorporate inexpensive carbon source. In this study, raw wastewater (RW) from pig farm, that was not anaerobically digested, was utilized as exogenous carbon in both A/O and SBR aerobic reactor to treat liquid digestate with high ammonia nitrogen and low C/N ratio. The results showed that N2O emission in SBR was higher than that of A/O process under the same nitrogen load. The N2O conversion in the biological nitrogen removal process was investigated by the strategy of integrating stable isotope method and metagenomics. The δO[18]-N2O, δN[15]-N2O, and SP values of the SBR were closer to the denitrification values of Ammonia-Oxidizing Bacteria (AOB) than those of A/O. The abundance of AOB in the SBR reactor was higher than that in the A/O reactor, while the abundance of denitrifying bacteria was lower. The amoA/B/C gene abundance in the SBR was greater than that in the A/O, and the NOS gene abundance was the opposite. The results indicated that both AOB denitrification and bacterial denitrification led to the increase of N2O emissions of the SBR.},
}
@article {pmid39232318,
year = {2024},
author = {Yadav, P and Kumari, SP and Hooda, S and Gupta, RK and Diwan, P},
title = {Comparative assessment of microbiome and resistome of influent and effluent of sewage treatment plant and common effluent treatment plant located in Delhi, India using shotgun approach.},
journal = {Journal of environmental management},
volume = {369},
number = {},
pages = {122342},
doi = {10.1016/j.jenvman.2024.122342},
pmid = {39232318},
issn = {1095-8630},
mesh = {India ; *Microbiota ; *Sewage/microbiology ; *Wastewater/microbiology ; Drug Resistance, Microbial/genetics ; Bacteria/genetics/drug effects ; Waste Disposal, Fluid ; },
abstract = {Antimicrobial resistance (AMR) is a significant threat that demands surveillance to identify and analyze trends of the emerging antibiotic resistance genes (ARGs) and potential microbial carriers. The influent of the wastewater treatment plants (WWTPs) reflects the microbes derived from the population and effluent being the source of dissemination of potential pathogenic microbes and AMR. The present study aimed to monitor microbial communities and antibiotic resistance genes in WWTPs employing a whole metagenome shotgun sequencing approach. The samples were collected from a sewage treatment plant (STP) and a common effluent treatment plant (CETP) in Delhi, India. The results showed the influent of STP to be rich in Bifidobacterium, Bacteroides, Escherichia, Arcobacter, and Pseudomonas residents of gut microbiota and known to cause diseases in humans and animals; whereas the CETP sample was abundant in Aeromonas, Escherichia, and Shewanella known to be involved in the degradation of different compounds. Interestingly, the effluent samples from both STPs and CETP were rich in microbial diversity, comprising organic and xenobiotic compound degrading and disease-causing bacteria, indicating the effluent being the source of dissemination of concerning bacteria to the environment. The functional profile at both sites displayed similarity with an abundance of housekeeping function genes as analyzed by Clusters of Orthologous Genes (COG), KEGG Orthology (KO), and subsystem databases. Resistome profiling by MEGARes showed the dominance of ARGs corresponding to beta-lactams having relative abundance ranging from 16% to 34% in all the metagenome datasets, followed by tetracycline (8%-16%), aminoglycosides (7%-9%), multi-drug (5%-9%), and rifampin (3%-9%). Also, AMR genes oxa, ant3-DPRIME, and rpoB, which are of clinical importance were predominantly and most prevalently present in all the samples. The presence of AMR in effluents from both types of treatment plants indicates that wastewater from both sources contributes to the spread of pathogenic bacteria and resistance genes, increasing the environmental AMR burden and therefore requires tertiary treatment before discharge. This work will facilitate further research towards the identification of suitable biomarkers for monitoring antibiotic resistance.},
}
@article {pmid39232205,
year = {2024},
author = {Quek, S and Hadermann, A and Wu, Y and De Coninck, L and Hegde, S and Boucher, JR and Cresswell, J and Foreman, E and Steven, A and LaCourse, EJ and Ward, SA and Wanji, S and Hughes, GL and Patterson, EI and Wagstaff, SC and Turner, JD and Parry, RH and Kohl, A and Heinz, E and Otabil, KB and Matthijnssens, J and Colebunders, R and Taylor, MJ},
title = {Diverse RNA viruses of parasitic nematodes can elicit antibody responses in vertebrate hosts.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {39232205},
issn = {2058-5276},
support = {V474923N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; 11L1323N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; G0A0522N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; BB/V011278/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; },
abstract = {Parasitic nematodes have an intimate, chronic and lifelong exposure to vertebrate tissues. Here we mined 41 published parasitic nematode transcriptomes from vertebrate hosts and identified 91 RNA viruses across 13 virus orders from 24 families in ~70% (28 out of 41) of parasitic nematode species, which include only 5 previously reported viruses. We observe widespread distribution of virus-nematode associations across multiple continents, suggesting an ancestral acquisition event and host-virus co-evolution. Characterization of viruses of Brugia malayi (BMRV1) and Onchocerca volvulus (OVRV1) shows that these viruses are abundant in reproductive tissues of adult parasites. Importantly, the presence of BMRV1 RNA in B. malayi parasites mounts an RNA interference response against BMRV1 suggesting active viral replication. Finally, BMRV1 and OVRV1 were found to elicit antibody responses in serum samples from infected jirds and infected or exposed humans, indicating direct exposure to the immune system.},
}
@article {pmid39232160,
year = {2024},
author = {Chen, J and Jia, Y and Sun, Y and Liu, K and Zhou, C and Liu, C and Li, D and Liu, G and Zhang, C and Yang, T and Huang, L and Zhuang, Y and Wang, D and Xu, D and Zhong, Q and Guo, Y and Li, A and Seim, I and Jiang, L and Wang, L and Lee, SMY and Liu, Y and Wang, D and Zhang, G and Liu, S and Wei, X and Yue, Z and Zheng, S and Shen, X and Wang, S and Qi, C and Chen, J and Ye, C and Zhao, F and Wang, J and Fan, J and Li, B and Sun, J and Jia, X and Xia, Z and Zhang, H and Liu, J and Zheng, Y and Liu, X and Wang, J and Yang, H and Kristiansen, K and Xu, X and Mock, T and Li, S and Zhang, W and Fan, G},
title = {Global marine microbial diversity and its potential in bioprospecting.},
journal = {Nature},
volume = {633},
number = {8029},
pages = {371-379},
pmid = {39232160},
issn = {1476-4687},
mesh = {*CRISPR-Cas Systems/genetics ; *Bioprospecting ; *Biodiversity ; *Aquatic Organisms/genetics ; Bacteria/genetics/classification ; Archaea/genetics/classification ; Genome, Bacterial/genetics ; Metagenome ; Genome, Archaeal/genetics ; Seawater/microbiology ; Phylogeny ; Oceans and Seas ; },
abstract = {The past two decades has witnessed a remarkable increase in the number of microbial genomes retrieved from marine systems[1,2]. However, it has remained challenging to translate this marine genomic diversity into biotechnological and biomedical applications[3,4]. Here we recovered 43,191 bacterial and archaeal genomes from publicly available marine metagenomes, encompassing a wide range of diversity with 138 distinct phyla, redefining the upper limit of marine bacterial genome size and revealing complex trade-offs between the occurrence of CRISPR-Cas systems and antibiotic resistance genes. In silico bioprospecting of these marine genomes led to the discovery of a novel CRISPR-Cas9 system, ten antimicrobial peptides, and three enzymes that degrade polyethylene terephthalate. In vitro experiments confirmed their effectiveness and efficacy. This work provides evidence that global-scale sequencing initiatives advance our understanding of how microbial diversity has evolved in the oceans and is maintained, and demonstrates how such initiatives can be sustainably exploited to advance biotechnology and biomedicine.},
}
@article {pmid39232089,
year = {2024},
author = {Melo, T and Sousa, CA and Delacour-Estrella, S and Bravo-Barriga, D and Seixas, G},
title = {Characterization of the microbiome of Aedes albopictus populations in different habitats from Spain and São Tomé.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {20545},
pmid = {39232089},
issn = {2045-2322},
mesh = {Animals ; *Aedes/microbiology ; Spain ; *Microbiota ; *Wolbachia/genetics/isolation &amp; purification/physiology ; Female ; *RNA, Ribosomal, 16S/genetics ; Mosquito Vectors/microbiology ; Ecosystem ; Male ; },
abstract = {The mosquito microbiome significantly influences vector competence, including in Aedes albopictus, a globally invasive vector. Describing the microbiome and Wolbachia strains of Ae. albopictus from different regions can guide area-specific control strategies. Mosquito samples from Spain and São Tomé were analyzed using 16S rRNA gene sequencing and metagenomic sequencing. Wolbachia infection patterns were observed by sex and population. Female mosquitoes were blood-fed, a factor considered in analyzing their microbiota. Results revealed a dominance of dual Wolbachia infections, strains A and B, in the microbiome of both populations of Ae. albopictus, especially among females. Both populations shared a core microbiome, although 5 and 9 other genera were only present in Spain and São Tomé populations, respectively. Genera like Pelomonas and Nevskia were identified for the first time in Aedes mosquitoes. This study is the first to describe the Ae. albopictus bacteriome in Spain and São Tomé, offering insights for the development of targeted mosquito control strategies. Understanding the specific microbiome composition can help in designing more effective interventions, such as microbiome manipulation and Wolbachia-based approaches, to reduce vector competence and transmission potential of these mosquitoes.},
}
@article {pmid39231974,
year = {2024},
author = {Oliver, T and Varghese, N and Roux, S and Schulz, F and Huntemann, M and Clum, A and Foster, B and Foster, B and Riley, R and LaButti, K and Egan, R and Hajek, P and Mukherjee, S and Ovchinnikova, G and Reddy, TBK and Calhoun, S and Hayes, RD and Rohwer, RR and Zhou, Z and Daum, C and Copeland, A and Chen, IA and Ivanova, NN and Kyrpides, NC and Mouncey, NJ and Del Rio, TG and Grigoriev, IV and Hofmeyr, S and Oliker, L and Yelick, K and Anantharaman, K and McMahon, KD and Woyke, T and Eloe-Fadrosh, EA},
title = {Coassembly and binning of a twenty-year metagenomic time-series from Lake Mendota.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {966},
pmid = {39231974},
issn = {2052-4463},
support = {DEB-2025982//NSF | BIO | Division of Environmental Biology (DEB)/ ; DEB-1344254//NSF | BIO | Division of Environmental Biology (DEB)/ ; MCB-0702395//NSF | BIO | Division of Molecular and Cellular Biosciences (MCB)/ ; WIS01516, WIS01789, WIS03004//United States Department of Agriculture | Agricultural Research Service (USDA Agricultural Research Service)/ ; DBI-2011002//NSF | BIO | Division of Biological Infrastructure (DBI)/ ; 89233218CNA000001//U.S. Department of Energy (DOE)/ ; DE-AC05-76RL01830//U.S. Department of Energy (DOE)/ ; DE-AC05-00OR22725//U.S. Department of Energy (DOE)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; 17-SC-20-SC//U.S. Department of Energy (DOE)/ ; },
mesh = {Bacteria/genetics/classification ; *Lakes/microbiology ; *Metagenome ; Metagenomics ; Phylogeny ; },
abstract = {The North Temperate Lakes Long-Term Ecological Research (NTL-LTER) program has been extensively used to improve understanding of how aquatic ecosystems respond to environmental stressors, climate fluctuations, and human activities. Here, we report on the metagenomes of samples collected between 2000 and 2019 from Lake Mendota, a freshwater eutrophic lake within the NTL-LTER site. We utilized the distributed metagenome assembler MetaHipMer to coassemble over 10 terabases (Tbp) of data from 471 individual Illumina-sequenced metagenomes. A total of 95,523,664 contigs were assembled and binned to generate 1,894 non-redundant metagenome-assembled genomes (MAGs) with ≥50% completeness and ≤10% contamination. Phylogenomic analysis revealed that the MAGs were nearly exclusively bacterial, dominated by Pseudomonadota (Proteobacteria, N = 623) and Bacteroidota (N = 321). Nine eukaryotic MAGs were identified by eukCC with six assigned to the phylum Chlorophyta. Additionally, 6,350 high-quality viral sequences were identified by geNomad with the majority classified in the phylum Uroviricota. This expansive coassembled metagenomic dataset provides an unprecedented foundation to advance understanding of microbial communities in freshwater ecosystems and explore temporal ecosystem dynamics.},
}
@article {pmid39231841,
year = {2024},
author = {Yi, P and Li, Q and Zhou, X and Liang, R and Ding, X and Wu, M and Wang, K and Li, J and Wang, W and Lu, G and Zhu, T},
title = {Inoculation of Saccharomyces cerevisiae for facilitating aerobic composting of acidified food waste.},
journal = {Environmental science and pollution research international},
volume = {31},
number = {43},
pages = {55507-55521},
pmid = {39231841},
issn = {1614-7499},
support = {2022-SF-147//Key Research and Development and Transformation Program of Qinghai Province of China/ ; 32272538//National Natural Science Foundation of China/ ; },
mesh = {*Saccharomyces cerevisiae ; *Composting ; Hydrogen-Ion Concentration ; Food ; Fermentation ; Aerobiosis ; Food Loss and Waste ; },
abstract = {In aerobic composting of food waste, acidification of the material (acidified food waste, AFW) often occurs and consequently leads to failure of fermentation initiation. In this study, we solved this problem by adding Saccharomyces cerevisiae inoculants. The results showed that the inoculation with S. cerevisiae effectively promoted the composting process. In 2 kg composting, inoculation with S. cerevisiae significantly elevated the pile temperatures by 4 ~ 14 °C, accompanied by a rapid increase in pH from 4.5 to 6.0. In 15 kg composting, total acid decreased faster and the thermophilic stage above 50 °C was prolonged by 3 days longer than in the control. The residual oxygen content in the reactor indicated that S. cerevisiae, which proliferated during composting, increased microbial activity and reduced ammonia emission during the thermophilic phase. Cell density analysis showed that compost inoculated with S. cerevisiae promoted thermophilic bacterial propagation. Metagenomic analysis showed that the dominant bacteria in the AFW compost were Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria, and the relative abundance of Bacillus, Thermobacillus, and Thermobifida increased when inoculated with S. cerevisiae. These results indicate that the inoculation of S. cerevisiae is an effective strategy to improve the aerobic composting process of AFW by accelerating the initial phase and altering microbial community structure in the thermophilic phase. Our findings suggest that S. cerevisiae can be applied to aerobic composting of organic wastes to effectively address the problem of acidification.},
}
@article {pmid39230701,
year = {2024},
author = {Hera, MR and Liu, S and Wei, W and Rodriguez, JS and Ma, C and Koslicki, D},
title = {Metagenomic functional profiling: to sketch or not to sketch?.},
journal = {Bioinformatics (Oxford, England)},
volume = {40},
number = {Suppl 2},
pages = {ii165-ii173},
pmid = {39230701},
issn = {1367-4811},
support = {R01 GM146462/GM/NIGMS NIH HHS/United States ; R01GM146462/GF/NIH HHS/United States ; },
mesh = {*Metagenomics/methods ; *Software ; *Algorithms ; *Metagenome/genetics ; Humans ; Microbiota/genetics ; Databases, Genetic ; },
abstract = {MOTIVATION: Functional profiling of metagenomic samples is essential to decipher the functional capabilities of microbial communities. Traditional and more widely used functional profilers in the context of metagenomics rely on aligning reads against a known reference database. However, aligning sequencing reads against a large and fast-growing database is computationally expensive. In general, k-mer-based sketching techniques have been successfully used in metagenomics to address this bottleneck, notably in taxonomic profiling. In this work, we describe leveraging FracMinHash (implemented in sourmash, a publicly available software), a k-mer-sketching algorithm, to obtain functional profiles of metagenome samples.<br><br>RESULTS: We show how pieces of the sourmash software (and the resulting FracMinHash sketches) can be put together in a pipeline to functionally profile a metagenomic sample. We named our pipeline fmh-funprofiler. We report that the functional profiles obtained using this pipeline demonstrate comparable completeness and better purity compared to the profiles obtained using other alignment-based methods when applied to simulated metagenomic data. We also report that fmh-funprofiler is 39-99&#xd7; faster in wall-clock time, and consumes up to 40-55&#xd7; less memory. Coupled with the KEGG database, this method not only replicates fundamental biological insights but also highlights novel signals from the Human Microbiome Project datasets.<br><br>This fast and lightweight metagenomic functional profiler is freely available and can be accessed here: https://github.com/KoslickiLab/fmh-funprofiler. All scripts of the analyses we present in this manuscript can be found on GitHub.},
}
@article {pmid39230289,
year = {2024},
author = {Flamholz, ZN and Li, C and Kelly, L},
title = {Improving viral annotation with artificial intelligence.},
journal = {mBio},
volume = {},
number = {},
pages = {e0320623},
doi = {10.1128/mbio.03206-23},
pmid = {39230289},
issn = {2150-7511},
abstract = {Viruses of bacteria, "phages," are fundamental, poorly understood components of microbial community structure and function. Additionally, their dependence on hosts for replication positions phages as unique sensors of ecosystem features and environmental pressures. High-throughput sequencing approaches have begun to give us access to the diversity and range of phage populations in complex microbial community samples, and metagenomics is currently the primary tool with which we study phage populations. The study of phages by metagenomic sequencing, however, is fundamentally limited by viral diversity, which results in the vast majority of viral genomes and metagenome-annotated genomes lacking annotation. To harness bacteriophages for applications in human and environmental health and disease, we need new methods to organize and annotate viral sequence diversity. We recently demonstrated that methods that leverage self-supervised representation learning can supplement statistical sequence representations for remote viral protein homology detection in the ocean virome and propose that consideration of the functional content of viral sequences allows for the identification of similarity in otherwise sequence-diverse viruses and viral-like elements for biological discovery. In this review, we describe the potential and pitfalls of large language models for viral annotation. We describe the need for new approaches to annotate viral sequences in metagenomes, the fundamentals of what protein language models are and how one can use them for sequence annotation, the strengths and weaknesses of these models, and future directions toward developing better models for viral annotation more broadly.},
}
@article {pmid39230261,
year = {2024},
author = {Tu, V and Ren, Y and Tanes, C and Mukhopadhyay, S and Daniel, SG and Li, H and Bittinger, K},
title = {A quantitative approach to measure and predict microbiome response to antibiotics.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0048824},
doi = {10.1128/msphere.00488-24},
pmid = {39230261},
issn = {2379-5042},
abstract = {UNLABELLED: Although antibiotics induce sizable perturbations in the human microbiome, we lack a systematic and quantitative method to measure and predict the microbiome's response to specific antibiotics. Here, we introduce such a method, which takes the form of a microbiome response index (MiRIx) for each antibiotic. Antibiotic-specific MiRIx values quantify the overall susceptibility of the microbiota to an antibiotic, based on databases of bacterial phenotypes and published data on intrinsic antibiotic susceptibility. We applied our approach to five published microbiome studies that carried out antibiotic interventions with vancomycin, metronidazole, ciprofloxacin, amoxicillin, and doxycycline. We show how MiRIx can be used in conjunction with existing microbiome analytical approaches to gain a deeper understanding of the microbiome response to antibiotics. Finally, we generate antibiotic response predictions for the oral, skin, and gut microbiome in healthy humans. Our approach is implemented as open-source software and is readily applied to microbiome data sets generated by 16S rRNA marker gene sequencing or shotgun metagenomics.<br><br>IMPORTANCE: Antibiotics are potent influencers of the human microbiome and can be a source for enduring dysbiosis and antibiotic resistance in healthcare. Existing microbiome data analysis methods can quantify perturbations of bacterial communities but cannot evaluate whether the differences are aligned with the expected activity of a specific antibiotic. Here, we present a novel method to quantify and predict antibiotic-specific microbiome changes, implemented in a ready-to-use software package. This has the potential to be a critical tool to broaden our understanding of the relationship between the microbiome and antibiotics.},
}
@article {pmid39230075,
year = {2024},
author = {Kim, N and Kim, CY and Ma, J and Yang, S and Park, DJ and Ha, SJ and Belenky, P and Lee, I},
title = {MRGM: an enhanced catalog of mouse gut microbial genomes substantially broadening taxonomic and functional landscapes.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2393791},
pmid = {39230075},
issn = {1949-0984},
support = {R01 DK125382/DK/NIDDK NIH HHS/United States ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Mice ; *Bacteria/classification/genetics/isolation &amp; purification ; *Genome, Bacterial ; Humans ; Phylogeny ; Diet ; },
abstract = {Mouse gut microbiome research is pivotal for understanding the human gut microbiome, providing insights into disease modeling, host-microbe interactions, and the dietary influence on the gut microbiome. To enhance the translational value of mouse gut microbiome studies, we need detailed and high-quality catalogs of mouse gut microbial genomes. We introduce the Mouse Reference Gut Microbiome (MRGM), a comprehensive catalog with 42,245 non-redundant mouse gut bacterial genomes across 1,524 species. MRGM marks a 40% increase in the known taxonomic diversity of mouse gut microbes, capturing previously underrepresented lineages through refined genome quality assessment techniques. MRGM not only broadens the taxonomic landscape but also enriches the functional landscape of the mouse gut microbiome. Using deep learning, we have elevated the Gene Ontology annotation rate for mouse gut microbial proteins from 3.2% with orthology to 60%, marking an over 18-fold increase. MRGM supports both DNA- and marker-based taxonomic profiling by providing custom databases, surpassing previous catalogs in performance. Finally, taxonomic and functional comparisons between human and mouse gut microbiota reveal diet-driven divergences in their taxonomic composition and functional enrichment. Overall, our study highlights the value of high-quality microbial genome catalogs in advancing our understanding of the co-evolution between gut microbes and their host.},
}
@article {pmid39229966,
year = {2024},
author = {Garner, E and Maile-Moskowitz, A and Angeles, LF and Flach, CF and Aga, DS and Nambi, I and Larsson, DGJ and Bürgmann, H and Zhang, T and Vikesland, PJ and Pruden, A},
title = {Metagenomic Profiling of Internationally Sourced Sewage Influents and Effluents Yields Insight into Selecting Targets for Antibiotic Resistance Monitoring.},
journal = {Environmental science &amp; technology},
volume = {58},
number = {37},
pages = {16547-16559},
pmid = {39229966},
issn = {1520-5851},
mesh = {*Sewage/microbiology ; *Drug Resistance, Microbial/genetics ; *Metagenomics ; *Wastewater/microbiology ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/drug effects ; },
abstract = {It has been debated whether wastewater treatment plants (WWTPs) primarily act to attenuate or amplify antibiotic resistance genes (ARGs). However, ARGs are highly diverse with respect to their resistance mechanisms, mobilities, and taxonomic hosts and therefore their behavior in WWTPs should not be expected to be universally conserved. We applied metagenomic sequencing to wastewater influent and effluent samples from 12 international WWTPs to classify the behavior of specific ARGs entering and exiting WWTPs. In total, 1079 different ARGs originating from a variety of bacteria were detected. This included ARGs that could be mapped to assembled scaffolds corresponding to nine human pathogens. While the relative abundance (per 16S rRNA gene) of ARGs decreased during treatment at 11 of the 12 WWTPs sampled and absolute abundance (per mL) decreased at all 12 WWTPs, increases in relative abundance were observed for 40% of the ARGs detected at the 12th WWTP. Also, the relative abundance of mobile genetic elements (MGE) increased during treatment, but the fraction of ARGs known to be transmissible between species decreased, thus demonstrating that increased MGE prevalence may not be generally indicative of an increase in ARGs. A distinct conserved resistome was documented in both influent and effluent across samples, suggesting that well-functioning WWTPs generally attenuate influent antibiotic resistance loads. This work helps inform strategies for wastewater surveillance of antibiotic resistance, highlighting the utility of tracking ARGs as indicators of treatment performance and relative risk reduction.},
}
@article {pmid39229615,
year = {2024},
author = {Zhang, L and Zhang, Z and Huang, J and Zhou, R and Wu, C},
title = {Revealing salt concentration for microbial balance and metabolite enrichment in secondary fortified fermented soy sauce: A multi-omics perspective.},
journal = {Food chemistry: X},
volume = {23},
number = {},
pages = {101722},
pmid = {39229615},
issn = {2590-1575},
abstract = {This study examined the impact of varying salt concentrations on microbiota, physicochemical properties, and metabolites in a secondary fortified fermentation process using multi-omics techniques. It aimed to determine the influence of salt stress on microbiota shifts and metabolic activities. The findings demonstrated that moderate salt reduction (MS) was found to enhance moromi's flavor and quality, while mitigating the negative effects of excessive low salt (LS). MS samples had 1.22, 1.13, and 2.92 times more amino acid nitrogen (AAN), non-volatiles, and volatiles, respectively, than high salt (HS) samples. In contrast, lactic acid and biogenic amines in LS samples were 1.56 g/100 g and 4115.11 mg/kg, respectively, decreasing to 0.15 g/100 g and 176.76 mg/kg in MS samples. Additionally, the contents of ethanol and small peptides increased in MS due to the growth of specific functional microorganisms such as Staphylococcus gallinarum, Weissella confusa, and Zygosaccharomyces rouxii, while food-borne pathogens were inhibited. Network analysis revealed that the core microbial interactions were enhanced in MS samples, promoting a balanced fermentation environment. Redundancy analysis (RDA) and correlation analyses underscored that the physicochemical properties significantly impacted bacterial community structure and the correlations between key microbes and flavor compounds. These findings provided a theoretical foundation for developing innovative reduced-salt fermentation techniques, contributing to the sustainable production of high-quality soy sauce.},
}
@article {pmid39229329,
year = {2024},
author = {Li, J and Liu, L and Gao, Z and Chuai, X and Liu, X and Zhang, X and Zhang, X and Su, X and Xu, Q and Deng, Z},
title = {Bronchoalveolar Lavage Fluid Metagenomic Second-Generation Sequencing Assists in Guiding the Treatment of Visceral Leishmaniasis: A Case Report.},
journal = {Infection and drug resistance},
volume = {17},
number = {},
pages = {3769-3775},
pmid = {39229329},
issn = {1178-6973},
abstract = {PURPOSE: The incidence of visceral leishmaniasis (VL), a global infectious disease, has been on the rise in China's Hebei province. When patients achieve clinical cure, they often do not reach an etiological cure, which may lead to recurrence of the disease. Here, we report a case of visceral leishmaniasis with a negative blood smear and bone marrow cytology.<br><br>PATIENTS AND METHODS: A 65-year-old man and bronchoalveolar lavage fluid mNGS.<br><br>RESULTS: A 65-year-old man developed a chronic fever, anorexia, splenomegaly, and pancytopenia. The blood metagenomic second-generation sequencing (mNGS) revealed Leishmania sequence readings, which led to the diagnosis of VL. After sodium antimony gluconate treatment, the blood smear and bone marrow cytology revealed no Leishmania bodies. However, pancytopenia and respiratory failure did not fully subside, and cardiotoxic damage emerged. The bronchoalveolar lavage fluid (BALF) mNGS was performed to detect the pathogen. Through BALF mNGS, Leishmania sequence was still detectable. Therefore, after the ECG returned to normal, antimony sodium gluconate was administered as a next course of treatment.<br><br>CONCLUSION: BALF mNGS may assist in evaluating the therapeutic efficacy of VL with respiratory failure, especially in patients with negative blood and bone marrow cytology.},
}
@article {pmid39229115,
year = {2024},
author = {Fan, P and Ni, M and Fan, Y and Ksiezarek, M and Fan, P},
title = {Predictive power of different Akkermansia phylogroups in clinical response to PD-1 blockade against non-small cell lung cancer.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.08.21.608814},
pmid = {39229115},
issn = {2692-8205},
abstract = {Immune checkpoint blockade has emerged as a promising form of cancer therapy. However, only some patients respond to checkpoint inhibitors, while a significant proportion of patients do not, calling for the discovery of reliable biomarkers. Recent studies reported the importance of the gut microbiome in the clinical response to PD-1 blockade against advanced non-small cell lung cancer (NSCLC), highlighting Akkermansia muciniphila as a candidate biomarker. Motivated by the genomic and phenotypic differences across Akkermansia muciniphila strains and Akkermansia (Akk) phylogroups (AmIa, AmIb, AmII, AmIII and AmIV), we analyzed fecal metagenomic sequencing data from three publicly available NSCLC cohorts (n=425). Encouragingly, we found that patients' responses to PD-1 blockade are significantly different across different Akk phylogroups, highlighting the relatively stronger association between AmIa and positive response than the other phylogroups. We built a machine learning model based on Akk gene profiles, which improved the predictive power and shed light on a group of Akk genes that may be associated with the response to PD-1 blockade. In summary, our study underlines the benefits of high-resolution analysis of Akk genomes in the search for biomarkers that may improve the prediction of patients' responses to cancer immunotherapy.},
}
@article {pmid39229008,
year = {2024},
author = {Clark, CM and Kwan, JC},
title = {Creating and leveraging bespoke large-scale knowledge graphs for comparative genomics and multi-omics drug discovery with SocialGene.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39229008},
issn = {2692-8205},
support = {R35 GM133776/GM/NIGMS NIH HHS/United States ; T15 LM007359/LM/NLM NIH HHS/United States ; },
abstract = {The rapid expansion of multi-omics data has transformed biological research, offering unprecedented opportunities to explore complex genomic relationships across diverse organisms. However, the vast volume and heterogeneity of these datasets presents significant challenges for analyses. Here we introduce SocialGene, a comprehensive software suite designed to collect, analyze, and organize multi-omics data into structured knowledge graphs, with the ability to handle small projects to repository-scale analyses. Originally developed to enhance genome mining for natural product drug discovery, SocialGene has been effective across various applications, including functional genomics, evolutionary studies, and systems biology. SocialGene's concerted Python and Nextflow libraries streamline data ingestion, manipulation, aggregation, and analysis, culminating in a custom Neo4j database. The software not only facilitates the exploration of genomic synteny but also provides a foundational knowledge graph supporting the integration of additional diverse datasets and the development of advanced search engines and analyses. This manuscript introduces some of SocialGene's capabilities through brief case studies including targeted genome mining for drug discovery, accelerated searches for similar and distantly related biosynthetic gene clusters in biobank-available organisms, integration of chemical and analytical data, and more. SocialGene is free, open-source, MIT-licensed, designed for adaptability and extension, and available from github.com/socialgene.},
}
@article {pmid39228743,
year = {2024},
author = {Jules, E and Decker, C and Bixler, BJ and Ahmed, A and Zhou, ZC and Arora, I and Tafesse, H and Dakanay, H and Bombin, A and Wang, E and Ingersoll, J and Bifulco, K and Frediani, JK and Parsons, R and Sullivan, J and Greenleaf, M and Waggoner, JJ and Martin, GS and Lam, WA and Piantadosi, A},
title = {Respiratory virus detection and sequencing from negative SARS-CoV-2 rapid antigen tests.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
pmid = {39228743},
support = {U54 EB027690/EB/NIBIB NIH HHS/United States ; UL1 TR002378/TR/NCATS NIH HHS/United States ; },
abstract = {Genomic epidemiology offers important insight into the transmission and evolution of respiratory viruses. We used metagenomic sequencing from negative SARS-CoV-2 antigen tests to identify a wide range of respiratory viruses and generate full genome sequences, offering a streamlined mechanism for broad respiratory virus genomic surveillance.},
}
@article {pmid39228385,
year = {2024},
author = {Xu, ZX and Zeng, B and Chen, S and Xiao, S and Jiang, LG and Li, X and Wu, YF and You, LX},
title = {Soil microbial community composition and nitrogen enrichment responses to the operation of electric power substation.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1453162},
pmid = {39228385},
issn = {1664-302X},
abstract = {The surge in global energy demand mandates a significant expansion of electric power substations. Nevertheless, the ecological consequences of electric power substation operation, particularly concerning the electromagnetic field, on soil microbial communities and nitrogen enrichment remain unexplored. In this study, we collected soil samples from six distinct sites at varying distances from an electric power substation in Xintang village, southeastern China, and investigated the impacts of electromagnetic field on the microbial diversity and community structures employing metagenomic sequencing technique. Our results showed discernible dissimilarities in the fungal community across the six distinct sites, each characterized by unique magnetic and electric intensities, whereas comparable variations were not evident within bacterial communities. Correlation analysis revealed a diminished nitrogen fixation capacity at the site nearest to the substation, characterized by low moisture content, elevated pH, and robust magnetic induction intensity and electric field intensity. Conversely, heightened nitrification processes were observed at this location compared to others. These findings were substantiated by the relative abundance of key genes associated with ammonium nitrogen and nitrate nitrogen production. This study provides insights into the relationships between soil microbial communities and the enduring operation of electric power substations, thereby contributing fundamental information essential for the rigorous environmental impact assessments of these facilities.},
}
@article {pmid39227168,
year = {2024},
author = {Salmaso, N and Cerasino, L and Pindo, M and Boscaini, A},
title = {Taxonomic and functional metagenomic assessment of a Dolichospermum bloom in a large and deep lake south of the Alps.},
journal = {FEMS microbiology ecology},
volume = {100},
number = {10},
pages = {},
pmid = {39227168},
issn = {1574-6941},
support = {CN00000033//European Union/ ; },
mesh = {*Lakes/microbiology ; *Metagenomics ; *Metagenome ; *Phylogeny ; Eutrophication ; Cyanobacteria/genetics/classification/growth &amp; development/metabolism ; Aphanizomenon/genetics/growth &amp; development/metabolism ; },
abstract = {Untargeted genetic approaches can be used to explore the high metabolic versatility of cyanobacteria. In this context, a comprehensive metagenomic shotgun analysis was performed on a population of Dolichospermum lemmermannii collected during a surface bloom in Lake Garda in the summer of 2020. Using a phylogenomic approach, the almost complete metagenome-assembled genome obtained from the analysis allowed to clarify the taxonomic position of the species within the genus Dolichospermum and contributed to frame the taxonomy of this genus within the ADA group (Anabaena/Dolichospermum/Aphanizomenon). In addition to common functional traits represented in the central metabolism of photosynthetic cyanobacteria, the genome annotation uncovered some distinctive and adaptive traits that helped define the factors that promote and maintain bloom-forming heterocytous nitrogen-fixing Nostocales in oligotrophic lakes. In addition, genetic clusters were identified that potentially encode several secondary metabolites that were previously unknown in the populations evolving in the southern Alpine Lake district. These included geosmin, anabaenopetins, and other bioactive compounds. The results expanded the knowledge of the distinctive competitive traits that drive algal blooms and provided guidance for more targeted analyses of cyanobacterial metabolites with implications for human health and water resource use.},
}
@article {pmid39226954,
year = {2024},
author = {Zhang, Z and Yang, H and Linghu, M and Li, J and Chen, C and Wang, B},
title = {Cattle manure composting driven by a microbial agent: A coupled mechanism involving microbial community succession and organic matter conversion.},
journal = {The Science of the total environment},
volume = {952},
number = {},
pages = {175953},
doi = {10.1016/j.scitotenv.2024.175953},
pmid = {39226954},
issn = {1879-1026},
mesh = {*Composting ; *Manure/microbiology ; Animals ; Cattle ; Microbiota ; Soil Microbiology ; Bacillus/physiology ; },
abstract = {Aerobic composting has been used as a mainstream treatment technology for agricultural solid waste resourcing. In the present study, we investigated the effects and potential mechanisms of the addition of a microbial agent (LD) prepared by combining Bacillus subtilis, Bacillus paralicheniformis and Irpex lacteus in improving the efficiency of cattle manure composting. Our results showed that addition of 1.5 % LD significantly accelerated compost humification, i.e., the germination index and lignocellulose degradation rate of the final compost product reached values of 92.20 and 42.29 %, respectively. Metagenomic sequencing results showed that inoculation of cattle manure with LD increased the abundance of functional microorganisms. LD effectively promoted the production of humus precursors, which then underwent reactions through synergistic abiotic and biotic pathways to achieve compost humification. This research provides a theoretical basis for the study of microbial enhancement strategies and humus formation mechanisms in the composting of livestock manure.},
}
@article {pmid39226940,
year = {2024},
author = {Wang, M and Li, Y and Peng, H and Liu, K and Wang, X and Xiang, W},
title = {A cyclic shift-temperature operation method to train microbial communities of mesophilic anaerobic digestion.},
journal = {Bioresource technology},
volume = {412},
number = {},
pages = {131410},
doi = {10.1016/j.biortech.2024.131410},
pmid = {39226940},
issn = {1873-2976},
mesh = {Anaerobiosis ; *Temperature ; *Biofuels/microbiology ; Bioreactors/microbiology ; Methane/metabolism ; Methanosarcina/metabolism ; Microbiota/physiology ; },
abstract = {Temperature is the critical factor affecting the efficiency and cost of anaerobic digestion (AD). The current work develops a shift-temperature AD (STAD) between 35 °C and 55 °C, intending to optimise microbial community and promote substrate conversion. The experimental results showed that severe inhibition of biogas production occurred when the temperature was firstly increased stepwise from 35 °C to 50 °C, whereas no inhibition was observed at the second warming cycle. When the organic load rate was increased to 6.37 g VS/L/d, the biogas yield of the STAD reached about 400 mL/g VS, nearly double that of the constant-temperature AD (CTAD). STAD promoted the proliferation of Methanosarcina (up to 57.32 %), while severely suppressed hydrogenophilic methanogens. However, when the temperature was shifted to 35 °C, most suppressed species recovered quickly and the excess propionic acid was quickly consumed. Metagenomic analysis showed that STAD also promoted gene enrichment related to pathways metabolism, membrane functions, and methyl-based methanogenesis.},
}
@article {pmid39226813,
year = {2024},
author = {Guan, X and Xu, Y and Zhang, D and Li, H and Li, R and Shi, R},
title = {Microbial nitrogen transformation regulates pathogenic virulence in soil environment.},
journal = {Journal of environmental management},
volume = {369},
number = {},
pages = {122280},
doi = {10.1016/j.jenvman.2024.122280},
pmid = {39226813},
issn = {1095-8630},
mesh = {*Nitrogen/metabolism ; *Soil Microbiology ; Virulence ; *Soil/chemistry ; },
abstract = {Soil nitrogen addition induces the generation and proliferation of some bacterial virulence, yet the interactive mechanisms between the two remain unclear. Here we investigated the variation of virulence genes (VGs) abundance during soil nitrogen transformation, and explored the biological mechanism and key pathways involved in the regulation of VGs by nitrogen transformation. The results showed that the diversity and abundance of virulence genes in soil under high nitrogen input (100 mg/kg) were markedly higher than those under low nitrogen input (50 mg/kg), suggesting a trade-off between the prevalence of virulence genes and nitrogen metabolism. Nutritional/metabolic factor, regulation, immune modulation and motility were the dominant virulence types. Linear regression analysis showed that soil nitrogen mineralization and nitrification rate were closely correlated with the abundance of virulence genes, mainly involving adherence, nutritional/metabolic factors and immune modulation (p < 0.05). Structural equations indicated that microbial community succession associated with nitrogen transformation largely contributed to the changes in VGs abundance. Metagenomic analysis revealed that major virulence genes pilE, pchB, and galE were regulated by nitrogen-functional genes gdh, ureC, and amoC, implying that microbial nitrogen transformation influences immune modulation, nutritional/metabolic factors, and adherence-like virulence. The meta-transcriptome reiterated their co-regulation, and the key pathway may be glutamate/urea> α-ketoglutarate/ammonia > pyruvate/amino acid. The outcome provides strong evidence on the linkage between microbial nitrogen transformation and pathogenic virulence factors development in the soil environment, which will aid in the effective suppression of the prevalence of soil pathogenic virulence.},
}
@article {pmid39226681,
year = {2024},
author = {Yin, Y and Zhu, P and Guo, Y and Li, Y and Chen, H and Liu, J and Sun, L and Ma, S and Hu, C and Wang, H},
title = {Enhancing lower respiratory tract infection diagnosis: implementation and clinical assessment of multiplex PCR-based and hybrid capture-based targeted next-generation sequencing.},
journal = {EBioMedicine},
volume = {107},
number = {},
pages = {105307},
pmid = {39226681},
issn = {2352-3964},
mesh = {Humans ; *Multiplex Polymerase Chain Reaction/methods/economics ; *High-Throughput Nucleotide Sequencing/methods ; *Respiratory Tract Infections/diagnosis/microbiology ; Male ; Female ; Middle Aged ; *Bronchoalveolar Lavage Fluid/microbiology ; Aged ; Adult ; Metagenomics/methods ; Sensitivity and Specificity ; Young Adult ; Computational Biology/methods ; Aged, 80 and over ; Retrospective Studies ; Adolescent ; },
abstract = {BACKGROUND: Shotgun metagenomic next-generation sequencing (mNGS) is widely used to detect pathogens in bronchoalveolar lavage fluid (BALF). However, mNGS is complex and expensive. This study explored the feasibility of targeted next-generation sequencing (tNGS) in distinguishing lower respiratory tract infections in clinical practice.<br><br>METHODS: We used 229 retrospective BALF samples to establish thresholds and diagnostic values in a prospective cohort of 251 patients. After target pathogen selection, primer and probe design, optimization experiments, and bioinformatics analysis, multiplex PCR-based tNGS (mp-tNGS) and hybrid capture-based tNGS (hc-tNGS), targeting 198 and 3060 pathogens (DNA and RNA co-detection workflow) were established and performed.<br><br>FINDINGS: mp-tNGS and hc-tNGS took 10.3 and 16&#xa0;h, respectively, with low sequencing data sizes of 0.1&#xa0;M and 1&#xa0;M reads, and test costs reduced to a quarter and half of mNGS. The LoDs of mp-tNGS and hc-tNGS were 50-450&#xa0;CFU/mL. mp-tNGS and hc-tNGS were highly accurate, with 86.5% and 87.3% (vs. 85.5% for mNGS) sensitivities and 90.0% and 88.0% (vs. 92.1% for mNGS) specificities. tNGS detection rates for casual pathogens were 84.3% and 89.5% (vs. 88.5% for mNGS), significantly higher than conventional microbiological tests (P&#xa0;<&#xa0;0.001). In seven samples, tNGS detected Pneumocystis jirovecii, a fungus not detected by mNGS. Whereas mNGS detected six samples with filamentous fungi (Rhizopus oryzae, Aureobasidium pullulans, Aspergillus niger complex, etc.) which missed by tNGS. The anaerobic bacteria as pathogen in eight samples was failed to detect by mp-tNGS.<br><br>INTERPRETATION: tNGS may offer a new, broad-spectrum, rapid, accurate and cost-effective approach to diagnosing respiratory infections.<br><br>FUNDING: National Natural Science Foundation of China (81625014 and 82202535).},
}
@article {pmid39226177,
year = {2024},
author = {Boulton, W and Fidan, FR and Denise, H and De Maio, N and Goldman, N},
title = {SWAMPy: simulating SARS-CoV-2 wastewater amplicon metagenomes.},
journal = {Bioinformatics (Oxford, England)},
volume = {40},
number = {9},
pages = {},
pmid = {39226177},
issn = {1367-4811},
mesh = {*Wastewater/virology ; *SARS-CoV-2/genetics/isolation &amp; purification ; *Metagenome ; *COVID-19/virology/diagnosis ; Metagenomics/methods ; Software ; Humans ; Genome, Viral ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {MOTIVATION: Tracking SARS-CoV-2 variants through genomic sequencing has been an important part of the global response to the pandemic and remains a useful tool for surveillance of the virus. As well as whole-genome sequencing of clinical samples, this surveillance effort has been aided by amplicon sequencing of wastewater samples, which proved effective in real case studies. Because of its relevance to public healthcare decisions, testing and benchmarking wastewater sequencing analysis methods is also crucial, which necessitates a simulator. Although metagenomic simulators exist, none is fit for the purpose of simulating the metagenomes produced through amplicon sequencing of wastewater.<br><br>RESULTS: Our new simulation tool, SWAMPy (Simulating SARS-CoV-2 Wastewater Amplicon Metagenomes with Python), is intended to provide realistic simulated SARS-CoV-2 wastewater sequencing datasets with which other programs that rely on this type of data can be evaluated and improved. Our tool is suitable for simulating Illumina short-read RT-PCR amplified metagenomes.<br><br>The code for this project is available at https://github.com/goldman-gp-ebi/SWAMPy. It can be installed on any Unix-based operating system and is available under the GPL-v3 license.},
}
@article {pmid39225809,
year = {2024},
author = {Sangodkar, N and Gonsalves, MJ},
title = {Role of Nitrifiers Associated with Mangrove clam Polymesoda Erosa in Bioremediation.},
journal = {Bulletin of environmental contamination and toxicology},
volume = {113},
number = {3},
pages = {38},
pmid = {39225809},
issn = {1432-0800},
mesh = {Animals ; *Biodegradation, Environmental ; *Bivalvia/metabolism/microbiology ; *Nitrification ; *Ammonia/metabolism ; *Wastewater/microbiology ; Water Pollutants, Chemical/metabolism ; Nitrites/metabolism ; Nitrates/metabolism ; Waste Disposal, Fluid/methods ; },
abstract = {Polymesoda erosa is a mangrove clam known for its water filtration ability. This clam was investigated for its bioremediation potential and growth in synthetic wastewater during 40 days of incubation. Variation in the nutrient composition of water, biochemical composition of the clams, and metagenomic analysis of the microorganisms associated with clam tissue were carried out. Significant differences in the concentration of ammonia (p ≤ 0.01), nitrite (p ≤ 0.001), and nitrate (p ≤ 0.05) in the wastewater were observed between day 0 and day 40. A reduction of approximately 89% in ammonia concentration at the end of the experiment was recorded indicating nitrification activity. However, biochemical parameters showed negligible differences before and after the incubation experiment. Thus suggesting that the chemosynthetic-based nutrition aids in the survival of the clam as no organic matter was added to the medium. The substantial decline in levels of ammonia in the presence of clams as compared to its absence suggests the significant role of clams in improving the water quality. Furthermore, the metagenomic analysis of the gill tissue of P. erosa revealed ~ 50% of the microbial population to consist of nitrifiers. The study highlights the contribution by the nitrifers associated with the clams not only to its growth and resilience but also to bioremediation.},
}
@article {pmid39225513,
year = {2024},
author = {Han, K and Kuo, B and Khalili, H and Staller, K},
title = {Metagenomics analysis reveals unique gut microbiota signature of slow-transit constipation.},
journal = {Clinical and translational gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.14309/ctg.0000000000000766},
pmid = {39225513},
issn = {2155-384X},
support = {K23 DK120945/DK/NIDDK NIH HHS/United States ; KSN2022210 and KSN2211010//Korea Institute of Oriental Medicine/ ; },
abstract = {INTRODUCTION: Altered gut microbiota may play a role in slow-transit constipation (STC). We conducted a study of gut microbiota composition and functionality in STC using metagenomic analyses.<br><br>METHODS: We assembled a clinical cohort of 24 patients with STC physiology age- and sex-matched to 24 controls. We performed shotgun metagenomic sequencing followed by prediction of metabolite composition from functional profiles.<br><br>RESULTS: In a middle-aged (mean 55.3 years), predominantly female cohort, there were no significant differences in &#x3b1; diversity indices, but permutational multivariate analysis of variance analysis showed significant between-group differences (R2=0.050, p<0.001) between STC patients and controls. Gordonibacter pamelaeae, Bifidobacterium longum, Firmicutes bacterium CAG 94, and Anaerotruncus colihominis were more abundant in STC, while Coprococcus comes and Roseburia intestinalis were more abundant in controls. Gut-derived metabolites varying in STC relative to controls were related to bile acid and cholesterol metabolism.<br><br>DISCUSSION: We found a unique metagenomic and metabolomic signature of STC.},
}
@article {pmid39224904,
year = {2024},
author = {Li, Q and Li, M and Wang, S and Geater, AF and Dai, J},
title = {Clinical Diagnostic Challenge in a Case of Disseminated Talaromyces marneffei Infection Misdiagnosed Initially as Pulmonary Tuberculosis: A Case Report and Literature Review.},
journal = {Infection and drug resistance},
volume = {17},
number = {},
pages = {3751-3757},
pmid = {39224904},
issn = {1178-6973},
abstract = {This case reports a middle-aged male patient who was HIV-negative and initially misdiagnosed as pulmonary tuberculosis but was eventually diagnosed with disseminated Talaromyces marneffei (T. marneffei) infection by next-generation sequencing. The patient presented with respiratory symptoms, recurrent bone pain, and subcutaneous masses as the main symptoms. After one year of antifungal treatment, the symptoms improved obviously, but the symptoms recurred after two weeks of drug withdrawal, and the symptoms were relieved after re-administration of antifungal drugs again. This report highlights the need for the rapid evaluation of fungal infections with metagenomic next-generation sequencing (mNGS) in patients with an inadequate diagnostic basis for tuberculosis infection or a poor response to antituberculosis drugs. In addition, long-term follow-up is needed to observe disease recurrence in patients with disseminated T. marneffei infection.},
}
@article {pmid39224706,
year = {2024},
author = {Sun, L and Zhang, K and Liu, Y and Che, L and Zhang, P and Wang, B and Du, N},
title = {Metagenomic next-generation sequencing targeted and metagenomic next-generation sequencing for pulmonary infection in HIV-infected and non-HIV-infected individuals.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1438982},
pmid = {39224706},
issn = {2235-2988},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *HIV Infections/complications/virology ; Male ; Female ; *Metagenomics/methods ; *Bronchoalveolar Lavage Fluid/microbiology/virology ; Middle Aged ; Adult ; Bacteria/genetics/isolation &amp; purification/classification ; Aged ; Sensitivity and Specificity ; Viruses/genetics/isolation &amp; purification/classification ; Metagenome ; Respiratory Tract Infections/virology/microbiology/diagnosis ; },
abstract = {BACKGROUND: When individuals infected with human immunodeficiency virus (HIV) experience pulmonary infections, they often exhibit severe symptoms and face a grim prognosis. Consequently, early, rapid, and accurate pathogen diagnosis is vital for informing effective treatment strategies. This study aimed to use metagenomic next-generation sequencing (mNGS) and targeted mNGS (tNGS) to elucidate the characteristics of pulmonary infections in HIV and non-HIV individuals.<br><br>METHODS: This study enrolled 90 patients with pulmonary infection at the Department of Infectious Diseases of The First Hospital of Jilin University from June 2022 to May 2023, and they were divided into HIV (n=46) and non-HIV (n=44) infection groups. Their bronchoalveolar lavage fluid (BALF) was collected for mNGS analysis to evaluate the differences in pulmonary infection pathogens, and tNGS detection was performed on BALF samples from 15 HIV-infected patients.<br><br>RESULTS: A total of 37 pathogens were identified in this study, including 21 bacteria, 5 fungi, 5 viruses, 5 mycobacteria, and 1 mycoplasma. The sensitivity of mNGS was 78.9% (71/90), which is significantly higher than that of conventional methods (CTM) (39/90, P=1.5E-8). The combination of mNGS with CTM can greatly enhance the sensitivity of pathogen detection. The prevalence of Pneumocystis jirovecii (82.6% vs. 9.1%), cytomegalovirus (CMV) (58.7% vs. 0%), and Epstein-Barr virus (EBV) (17.4% vs. 2.3%) was significantly higher in the HIV infection group than in the non-HIV infection group (P<0.05). Although no statistically significant difference was observed, the detection rate of Mycobacteria was higher in HIV-infected patients (17.4%) than in the non-HIV group (6.8%). Furthermore, the tNGS results of BALF from 15 HIV-infected patients were not entirely consistent with the mNGS results., and the concordance rate of tNGS for the detection of main pathogens reached 86.7% (13/15).<br><br>CONCLUSION: Next-generation sequencing (NGS) can accurately detect pathogens in the BALF of patients with pulmonary infection. The sensitivity of tNGS is comparable to that of mNGS. Therefore, this technique should be promoted in the clinic for better patient outcomes.},
}
@article {pmid39224703,
year = {2024},
author = {Shi, Y and Zhang, W and Li, L and Wu, W and Li, M and Xiao, K and Wang, K and Sheng, Z and Xie, F and Wang, X and Shi, X and Tong, Y and Xie, L},
title = {Evaluation of phage-based decontamination in respiratory intensive care unit environments using ddPCR and 16S rRNA targeted sequencing techniques.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1442062},
pmid = {39224703},
issn = {2235-2988},
mesh = {*RNA, Ribosomal, 16S/genetics ; *Klebsiella pneumoniae/virology/genetics ; *Intensive Care Units ; *Decontamination/methods ; *Bacteriophages/genetics ; Humans ; Polymerase Chain Reaction/methods ; Cross Infection/prevention &amp; control/microbiology ; Disinfectants/pharmacology ; Klebsiella Infections/prevention &amp; control/microbiology ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Klebsiella pneumoniae is a major cause of hospital-acquired infections (HAIs), primarily spread through environmental contamination in hospitals. The effectiveness of current chemical disinfectants is waning due to emerging resistance, which poses environmental hazards and fosters new resistance in pathogens. Developing environmentally friendly and effective disinfectants against multidrug-resistant organisms is increasingly important.<br><br>METHODS: This study developed a bacteriophage cocktail targeting two common carbapenem-resistant Klebsiella pneumoniae (CRKP) strains, ST11 KL47 and ST11 KL64. The cocktail was used as an adjunctive disinfectant in a hospital's respiratory intensive care unit (RICU) via ultrasonic nebulization. Digital PCR was used to quantify CRKP levels post-intervention. The microbial community composition was analyzed via 16S rRNA sequencing to assess the intervention's impact on overall diversity.<br><br>RESULTS: The phage cocktail significantly reduced CRKP levels within the first 24 hours post-treatment. While a slight increase in pathogen levels was observed after 24 hours, they remained significantly lower than those treated with conventional disinfectants. 16S rRNA sequencing showed a decrease in the target pathogens' relative abundance, while overall species diversity remained stable, confirming that phages selectively target CRKP without disrupting ecological balance.<br><br>DISCUSSION: The findings highlight the efficacy and safety of phage-based biocleaners as a sustainable alternative to conventional disinfectants. Phages selectively reduce multidrug-resistant pathogens while preserving microbial diversity, making them a promising tool for infection control.},
}
@article {pmid39224188,
year = {2024},
author = {Looijesteijn, E and Schoemaker, MH and van den Belt, M and Hester, ER and Kortman, GAM and Viskaal-van Dongen, M and Nauta, A},
title = {A double-blind intervention trial in healthy women demonstrates the beneficial impact on Bifidobacterium with low dosages of prebiotic galacto-oligosaccharides.},
journal = {Frontiers in nutrition},
volume = {11},
number = {},
pages = {1440319},
pmid = {39224188},
issn = {2296-861X},
abstract = {INTRODUCTION: Galacto-oligosaccharides (GOS) are well-substantiated prebiotic substrates. Multiple studies have demonstrated a positive impact of GOS on gut microbiota composition and activity, so-far mainly related to Bifidobacterium. However, data on the beneficial impact at lower dosages in a healthy female population are limited. The primary aim of the current study was to reveal the effect of low dosages (1.3 and 2.0 g) of GOS on fecal Bifidobacterium abundance in healthy women. Other outcomes included the effect of low dosage of GOS on overall fecal microbiota composition and on self-perceived GI comfort, sleep quality and mental wellbeing.<br><br>METHOD: Eighty-eight healthy women (42-70&#x2009;years, BMI 18.7-30 kg/m[2]) were included in this randomized, parallel, double-blind study of 6&#x2009;weeks. The participants were stratified for fiber intake, BMI and age and randomized to consume either 1.3 or 2.0&#x2009;g of GOS per day for 3&#x2009;weeks after a control period of 3&#x2009;weeks without any intervention. Fecal samples were collected for shotgun metagenomics sequencing at the start (t&#x2009;=&#x2009;-3) and end (t&#x2009;=&#x2009;0) of the control period and at the end of the intervention period (t&#x2009;=&#x2009;3). Self-perceived gut comfort, sleep quality, and mental wellbeing were assessed weekly. Hierarchical clustering of principal components was applied to data collected from study participants.<br><br>RESULTS: The relative abundance of Bifidobacterium in feces increased significantly after 3&#x2009;weeks of daily consumption of both 1.3&#x2009;g (p&#x2009;<&#x2009;0.01) and 2.0&#x2009;g GOS (p&#x2009;<&#x2009;0.01). This was accompanied by a significant shift in the overall microbiota composition for the dosage of 2.0&#x2009;g GOS (p&#x2009;<&#x2009;0.01). Participants that showed a larger increase in Bifidobacterium in the intervention period compared to the change in Bifidobacterium in the control period, defined as responders, showed a significant overall difference in initial fecal microbiota composition as compared to non-responders (p&#x2009;=&#x2009;0.04) and a trend towards lower baseline levels of Bifidobacterium in responders (p&#x2009;=&#x2009;0.10).<br><br>CONCLUSION: Daily consumption of a low dose of GOS can lead to an increase in the relative abundance of Bifidobacterium in feces of healthy women. Additionally, with 2.0&#x2009;g GOS, the enrichment of Bifidobacterium is accompanied with a shift in the overall microbiota composition.Clinical trial registration: clinicaltrials.gov, identifier NCT05762965.},
}
@article {pmid39222819,
year = {2024},
author = {Yang, X and Wen, D and Liu, Z and Zhang, Y and Danzengjicha, and Yixiduoji, and Huang, X and Li, B},
title = {Biofermentation of aquatic plants: Potential novel feed ingredients for dairy cattle production.},
journal = {The Science of the total environment},
volume = {952},
number = {},
pages = {175955},
doi = {10.1016/j.scitotenv.2024.175955},
pmid = {39222819},
issn = {1879-1026},
mesh = {Animals ; Cattle ; *Silage ; *Animal Feed/analysis ; Dairying ; Diet/veterinary ; Female ; Zea mays ; Bacillus subtilis ; Fermentation ; Rumen/metabolism ; },
abstract = {The study assessed the impacts of aquatic plant silages on feeding efficiency and dairy cattle health as an alternative to conventional corn silage under high altitude conditions. Mid-lactation Holstein cows were assigned to treatment groups according to a randomized complete block design of parity, previous 105-d milk yield, and body weight. Cows (n = 8 per group) were fed with aquatic plant silage inoculated with Bacillus subtilis (BS), Yeast (YS), or conventional corn silage without inoculants (control) in addition to [standard grain feed] for 75 consecutive days. BS and YS had higher protein contents than control silage (111.20 ± 7.68, 112.10 ± 6.83 vs 76.94 ± 3.48 g/kg DM), while feeding efficiency was comparable between treatments (1.07, 0.99, and 0.90, respectively). In addition, the addition of aquatic plant silage in ruminant diets enhanced immunity and antioxidant capacity when compared with control group. Metagenomic analysis showed similar composition in rumen microbiota between YS and control groups, with higher enrichment for energy and nitrogen utilization pathways in YS-treated cows. This study highlights the use of aquatic plant silage as an alternative feed for dairy cattle with higher protein than corn silage. Our results suggest YS or BS could potentially boost immune and antioxidant functions, improving adaptation to high-altitudes and reducing demand for high input corn production on the Qinghai-Tibetan Plateau.},
}
@article {pmid39222807,
year = {2024},
author = {Shi, X and Zhang, J and Wang, Q and Wang, K and Han, J and Hui, Y and Jin, X and Jin, P},
title = {The sewer advances: How to select eco-friendly pipe materials for environmental protection.},
journal = {The Science of the total environment},
volume = {952},
number = {},
pages = {175853},
doi = {10.1016/j.scitotenv.2024.175853},
pmid = {39222807},
issn = {1879-1026},
mesh = {*Biofilms ; Sewage/microbiology ; Waste Disposal, Fluid/methods ; Wastewater ; },
abstract = {Sewer pipe materials exhibit diverse inner-surface features, which can affect the attachment of biofilm and influence microbial metabolic processes. To investigate the role of the type of pipe material on the composition and metabolic capabilities of the adhering microorganisms, three sets of urban sewers (High-Density Polyethylene Pipe (HDPE), Ductile Iron Pipe (DIP), and Concrete Pipe (CP)) were constructed. Measurements of biofilm thickness and environmental factors revealed that the thickest biofilm in CP pipes reached 2000 μm, with ORP values as low as -325 mV, indicating a more suitable anaerobic microbial habitat. High-throughput sequencing showed similar relative abundances of genera related to carbon and sulfur metabolism in the DIP and CP pipes, whereas HDPE exhibited only half the relative abundance compared to that found in the other pipes. To explore the impact of pipe materials on the mechanisms of microbial response, a metagenomic approach was used to investigate the biological transformation of carbon and sulfur in wastewater. The annotations of the crucial enzyme-encoding genes related to methyl coenzyme M and sulfite reductase in DIP and CP were 50 and 110, respectively, whereas HDPE exhibited lower counts (25 and 70, respectively). This resulted in significantly lower carbon and sulfur metabolism capabilities in the HDPE biofilm than in the other two pipes. The stability of wastewater quality during the transmission process in HDPE pipes reduces the metabolic generation of toxic and harmful gases within the pipes, favoring the preservation of carbon sources for sewer systems. This study reveals the variations in carbon and sulfur metabolism in wastewater pipe systems influenced by pipe materials and provides insights for designing future sewers.},
}
@article {pmid39222589,
year = {2024},
author = {Qiu, Y and Fu, Q and Yang, Y and Zhao, J and Li, J and Yi, F and Fu, X and Huang, Y and Tian, Z and Heitman, JL and Yao, Z and Dai, Z and Qiu, Y and Chen, H},
title = {Soil and stone terraces offset the negative impacts of sloping cultivation on soil microbial diversity and functioning by protecting soil carbon.},
journal = {Journal of environmental management},
volume = {369},
number = {},
pages = {122339},
doi = {10.1016/j.jenvman.2024.122339},
pmid = {39222589},
issn = {1095-8630},
mesh = {*Soil Microbiology ; *Soil/chemistry ; *Carbon/metabolism ; Fungi/metabolism ; Bacteria/metabolism ; Nitrogen/metabolism ; },
abstract = {Cultivation of sloping land is a main cause for soil erosion. Conservation practices, such as soil and stone terraces, may reduce the impacts of erosion but their impacts on soil microbial diversity and functioning related to carbon (C) and nutrient metabolisms remain unclear. This study was conducted to evaluate the effects of slope gradients (5°, 8°, 15°, 25°) and conservation practices (cultivated, uncultivated, soil terrace, and stone terrace) on bacterial and fungal diversities, metagenomic and metabolomic functioning associated with basic soil properties. Our results showed that steep slopes at 25° significantly decreased soil pH, silt percentage, and bacterial and fungal abundances, but that soil and stone terraces increased soil organic C (SOC), silt and clay contents, and fungal abundance compared to sloping cultivated lands. In addition, soil and stone terraces increased both bacterial and fungal alpha diversities, and relative abundances of Crenarchaeota, Nitrospirota, and Latescibacterota, but reduced the proportions of Actinobacteriota and Patescibacteria, thus shifting microbial beta diversities, which were significantly associated with increased SOC and silt content. For metagenomics, soil and stone terraces greatly increased the relative abundance of functional genes related to Respiration, Virulence, disease and defense, Stress response, and nitrogen and potassium metabolisms, such as Denitrification and Potassium homeostasis. For soil metabolomics, a total of 22 soil metabolites was enriched by soil and stone terraces, such as Lipids and lipid-like molecules (Arachidonic acid, Gamma-Linolenic acid, and Pentadecanoic acid), and Organoheterocyclic compounds (Adenine, Laudanosine, Methylpyrazine, and Nicotinic acid). To sum up, soil and stone terraces could reduce some of the negative impacts of steep slope cultivation on soil microbial diversity as well as their metagenomic and metabolomic functioning related to C and nutrient metabolism useful for soil health improvement, potentially bolstering the impact of sustainable practices in erosion hotspots around the world.},
}
@article {pmid39222347,
year = {2024},
author = {Glendinning, L and Wu, Z and Vervelde, L and Watson, M and Balic, A},
title = {Infectious bronchitis virus vaccination, but not the presence of XCR1, is correlated with large differences in chicken caecal microbiota.},
journal = {Microbial genomics},
volume = {10},
number = {9},
pages = {},
doi = {10.1099/mgen.0.001289},
pmid = {39222347},
issn = {2057-5858},
mesh = {Animals ; *Chickens/microbiology ; *Infectious bronchitis virus/immunology/genetics ; *Cecum/microbiology ; *Gastrointestinal Microbiome ; Vaccination ; Poultry Diseases/microbiology/virology/immunology ; Coronavirus Infections/veterinary/prevention &amp; control/immunology ; Viral Vaccines/immunology/genetics ; Receptors, G-Protein-Coupled/genetics ; Metagenome ; Dendritic Cells/immunology ; Bacteria/classification/genetics ; Metagenomics ; },
abstract = {The chicken immune system and microbiota play vital roles in maintaining gut homeostasis and protecting against pathogens. In mammals, XCR1+ conventional dendritic cells (cDCs) are located in the gut-draining lymph nodes and play a major role in gut homeostasis. These cDCs sample antigens in the gut luminal contents and limit the inflammatory response to gut commensal microbes by generating appropriate regulatory and effector T-cell responses. We hypothesized that these cells play similar roles in sustaining gut homeostasis in chickens, and that chickens lacking XCR1 were likely to contain a dysbiotic caecal microbiota. Here we compare the caecal microbiota of chickens that were either heterozygous or homozygous XCR1 knockouts, that had or had not been vaccinated for infectious bronchitis virus (IBV). We used short-read (Illumina) and long-read (PacBio HiFi) metagenomic sequencing to reconstruct 670 high-quality, strain-level metagenome assembled genomes. We found no significant differences between alpha diversity or the abundance of specific microbial taxa between genotypes. However, IBV vaccination was found to correlate with significant differences in the richness and beta diversity of the microbiota, and to the abundance of 40 bacterial genera. In conclusion, we found that a lack of XCR1 was not correlated with significant changes in the chicken microbiota, but IBV vaccination was.},
}
@article {pmid39222062,
year = {2024},
author = {Acheampong, DA and Jenjaroenpun, P and Wongsurawat, T and Kurilung, A and Pomyen, Y and Kandel, S and Kunadirek, P and Chuaypen, N and Kusonmano, K and Nookaew, I},
title = {CAIM: coverage-based analysis for identification of microbiome.},
journal = {Briefings in bioinformatics},
volume = {25},
number = {5},
pages = {},
pmid = {39222062},
issn = {1477-4054},
support = {P20 GM125503/GM/NIGMS NIH HHS/United States ; R01 CA143130/CA/NCI NIH HHS/United States ; P20GM125503//National Institute of General Medical Sciences of the National Institutes of Health/ ; R01CA143130/NH/NIH HHS/United States ; },
mesh = {Humans ; *Microbiota/genetics ; *Metagenomics/methods ; Computational Biology/methods ; Metagenome ; High-Throughput Nucleotide Sequencing/methods ; Software ; Algorithms ; Sequence Analysis, DNA/methods ; },
abstract = {Accurate taxonomic profiling of microbial taxa in a metagenomic sample is vital to gain insights into microbial ecology. Recent advancements in sequencing technologies have contributed tremendously toward understanding these microbes at species resolution through a whole shotgun metagenomic approach. In this study, we developed a new bioinformatics tool, coverage-based analysis for identification of microbiome (CAIM), for accurate taxonomic classification and quantification within both long- and short-read metagenomic samples using an alignment-based method. CAIM depends on two different containment techniques to identify species in metagenomic samples using their genome coverage information to filter out false positives rather than the traditional approach of relative abundance. In addition, we propose a nucleotide-count-based abundance estimation, which yield lesser root mean square error than the traditional read-count approach. We evaluated the performance of CAIM on 28 metagenomic mock communities and 2 synthetic datasets by comparing it with other top-performing tools. CAIM maintained a consistently good performance across datasets in identifying microbial taxa and in estimating relative abundances than other tools. CAIM was then applied to a real dataset sequenced on both Nanopore (with and without amplification) and Illumina sequencing platforms and found high similarity of taxonomic profiles between the sequencing platforms. Lastly, CAIM was applied to fecal shotgun metagenomic datasets of 232 colorectal cancer patients and 229 controls obtained from 4 different countries and 44 primary liver cancer patients and 76 controls. The predictive performance of models using the genome-coverage cutoff was better than those using the relative-abundance cutoffs in discriminating colorectal cancer and primary liver cancer patients from healthy controls with a highly confident species markers.},
}
@article {pmid39221872,
year = {2024},
author = {Wang, Z and Xu, M and Li, Q and Lu, S and Liu, Z},
title = {Subchronic Chloroform Exposure Causes Intestinal Damage and Induces Gut Microbiota Disruption and Metabolic Dysregulation in Mice.},
journal = {Environmental toxicology},
volume = {},
number = {},
pages = {},
doi = {10.1002/tox.24417},
pmid = {39221872},
issn = {1522-7278},
support = {LH2021C095//Natural Science Foundation of Heilongjiang Province of China/ ; 1452TD008//Heilongjiang Provincial Department of Education filing project/ ; 1451TD002//Heilongjiang Provincial Department of Education filing project/ ; },
abstract = {Chloroform is a prevalent toxic environmental pollutant in urban settings, posing risks to human health through exposure via various mediums such as air and tap water. The gut microbiota plays a pivotal role in maintaining host health. However, there is a paucity of research elucidating the impact of chloroform exposure on the gut microbiota. In this investigation, 18 SPF Kunming female mice were stratified into three groups (n = 6) and subjected to oral gavage with chloroform doses equivalent to 0, 50, and 150 mg/kg of body weight over 30 days. Our findings demonstrate that subchronic chloroform exposure significantly perturbs hematological parameters in mice and induces histopathological alterations in cecal tissues, consequently engendering marked disparities in the functional composition of cecal microbiota and metabolic equilibrium of cecal contents. Ultimately, our investigation revealed a statistically robust correlation, exhibiting a high degree of significance, between the intestinal microbiome composition and the metabolites that were differentially expressed consequent to chloroform exposure.},
}
@article {pmid39221224,
year = {2024},
author = {Song, CY and Yang, J and Jiang, S and Du, GL},
title = {HNF1β, LHX1, and GGNBP2 deletion contributed to kidney and reproductive dysfunction in 17q12 deletion syndrome: evidence from a case report.},
journal = {Frontiers in genetics},
volume = {15},
number = {},
pages = {1391804},
pmid = {39221224},
issn = {1664-8021},
abstract = {17q12 deletion syndrome is a chromosomal abnormality, where there is a small missing piece (deletion) of genetic material on the long arm (q) of chromosome 17. Sign and symptoms can vary widely among different patients. Recently, a patient was diagnosed with 17q12 deletion syndrome in our hospital, and the clinical characteristics presented as absence of the right kidney, compensatory hypertrophy of the left kidney, multiple small cysts in the left kidney, pancreatic atrophy, hypomagnesemia, bowed uterus, multiple follicular cysts in both lobes of the thyroid gland, and maturity-onset diabetes of the young type 5 (MODY-5). A 1.5-Mb deletion with haploinsufficiency for 20 genes within the 17q12 region was found through copy number variation (CNV) analysis based on metagenomic next-generation sequencing (mNGS) technology. In addition to HNF1B absence, the LIM-class homeobox 1 transcription factor (LHX1) and GGNBP2 absence was also involved in regulation of kidney development and the reproductive system through bioinformatics analysis. The inheriting risk of 17q12 deletion syndrome is about 50%, and it is recommended to provide genetic counseling to all patients who are suspected or diagnosed with the syndrome.},
}
@article {pmid39221074,
year = {2024},
author = {Qiu, Z and Zhu, Y and Zhang, Q and Qiao, X and Mu, R and Xu, Z and Yan, Y and Wang, F and Zhang, T and Zhuang, WQ and Yu, K},
title = {Unravelling biosynthesis and biodegradation potentials of microbial dark matters in hypersaline lakes.},
journal = {Environmental science and ecotechnology},
volume = {20},
number = {},
pages = {100359},
pmid = {39221074},
issn = {2666-4984},
abstract = {Biosynthesis and biodegradation of microorganisms critically underpin the development of biotechnology, new drugs and therapies, and environmental remediation. However, most uncultured microbial species along with their metabolic capacities in extreme environments, remain obscured. Here we unravel the metabolic potential of microbial dark matters (MDMs) in four deep-inland hypersaline lakes in Xinjiang, China. Utilizing metagenomic binning, we uncovered a rich diversity of 3030 metagenome-assembled genomes (MAGs) across 82 phyla, revealing a substantial portion, 2363 MAGs, as previously unclassified at the genus level. These unknown MAGs displayed unique distribution patterns across different lakes, indicating a strong correlation with varied physicochemical conditions. Our analysis revealed an extensive array of 9635 biosynthesis gene clusters (BGCs), with a remarkable 9403 being novel, suggesting untapped biotechnological potential. Notably, some MAGs from potentially new phyla exhibited a high density of these BGCs. Beyond biosynthesis, our study also identified novel biodegradation pathways, including dehalogenation, anaerobic ammonium oxidation (Anammox), and degradation of polycyclic aromatic hydrocarbons (PAHs) and plastics, in previously unknown microbial clades. These findings significantly enrich our understanding of biosynthesis and biodegradation processes and open new avenues for biotechnological innovation, emphasizing the untapped potential of microbial diversity in hypersaline environments.},
}
@article {pmid39220937,
year = {2024},
author = {Wei, L and Luo, J and Wu, W and Yin, J and Sun, Z and Xu, X and Gong, W and Xu, J},
title = {Clinical diagnostic value of metagenomic next-generation sequencing in patients with acute infection in emergency department.},
journal = {Heliyon},
volume = {10},
number = {16},
pages = {e35802},
pmid = {39220937},
issn = {2405-8440},
abstract = {OBJECTIVE: To explore the value of metagenomic next-generation sequencing (mNGS) and culture in microbial diagnosis of patients with acute infection.<br><br>METHODS: We retrospectively analyzed 206 specimens from 163 patients who were admitted to the emergency department of The First Affiliated Hospital of Sun Yat-sen University between July 2020, and July 2021. We evaluated the diagnostic efficacy of mNGS and in-hospital traditional culture.<br><br>RESULTS: The total positive rate of mNGS was significantly higher than that culture methods (71.4 % vs 40.8 %, p&#xa0;<&#xa0;0.001), while the sensitivity and accuracy of mNGS were found to be 92.9&#xa0;% and 88.2&#xa0;% respectively. However, culture exhibited superior specificity with a value of 92.6&#xa0;% compared to 75.9&#xa0;% for mNGS. The detection efficiency of mNGS and culture for fungi was comparable, but mNGS showed superior performance for bacterial detection. In the analysis of sepsis samples, mNGS outperformed traditional culture methods in diagnosing various types of samples, especially for sputum and bronchoalveolar lavage fluid. Among the identified infections, bacterial infections were the most common single infection (37.5&#xa0;%). Additionally, bacterial-fungal infections represented the most prevalent form of mixed infection (77.3&#xa0;%). Candida albicans and Staphylococcus aureus were identified as the predominant pathogens in the survival and death groups, respectively. No significant differences in microbial diversity were observed.<br><br>CONCLUSION: Compared to culture methods, mNGS demonstrates superior positive rates, sensitivity, and accuracy in the rapid detection of acute infections, particularly in critically ill patients such as those with sepsis. This capability establishes a foundation for the swift and precise identification of pathogens, allowing for the analysis of clinical indicators and patient prognosis based on the extensive data generated from mNGS.},
}
@article {pmid39220283,
year = {2024},
author = {Ding, Y and Liu, G and Li, Q and Zou, L and Dai, J and Chongsuvivatwong, V},
title = {Distribution characteristics of human herpes viruses in the lower respiratory tract and their impact on 30-day mortality in community-acquired pneumonia patients.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1436509},
pmid = {39220283},
issn = {2235-2988},
mesh = {Humans ; Roseolovirus Infections/diagnosis ; *Bronchoalveolar Lavage Fluid/virology ; Male ; Female ; Adult ; Middle Aged ; Aged ; *Pneumonia/microbiology/mortality/therapy/virology ; Severity of Illness Index ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; *Herpesviridae/genetics/isolation &amp; purification ; },
abstract = {Human herpes viruses (HHVs) are commonly detected in community-acquired pneumonia (CAP) patients, particularly those with complex complications, attracting increased attention from clinical practitioners. However, the significance of detecting HHVs in bronchoalveolar lavage fluid (BALF) with CAP patients is still unclear. This study retrospectively analyzed BALF samples from 64 CAP patients at the Kunming Third People's Hospital between August 2021 and December 2023. Metagenomic next generation sequencing (mNGS) was conducted on BALF samples during CAP onset. Multivariate Cox regression models were used to identify independent risk factors for 30-day all-cause mortality in CAP. HHVs were found in 84.4% of CAP patients, which were the most common pathogens (45.1%), followed by bacteria (30.2%) and fungi (11.5%). Bacterial-viral co-infections were most common, occurring in 39 patients. Notably, there was no significant difference in HHV presence between severe and non-severe CAP patients (EBV: P = 0.431, CMV: P = 0.825), except for HHV-7 (P = 0.025). In addition, there was no significant difference in the 30-day mortality between HHV positive and HHV negative groups (P = 0.470), as well as between the HHV-7 positive and HHV-7 negative groups (P = 0.910). However, neither HHVs nor HHV-7 was independent risk factors for 30-day mortality in CAP patients (HHVs: HR 1.171, P = 0.888; HHV-7: HR 1.947, P = 0.382). In summary, among the prevalent presence of multiple HHVs, EBV and CMV were the most prevalent in CAP patients. Patients with sCAP were more susceptible to HHV-7 than those with non-sCAP. These results provide valuable insights for clinicians in guiding appropriate interventions for CAP treatment.},
}
@article {pmid39219687,
year = {2024},
author = {Peng, Z and Wang, P and Luo, X and Deng, Q and Yang, Z and Wu, J and Xian, W and Yan, W and Mou, X and Yuan, Y and Li, W and Li, J},
title = {Community structure and carbon metabolism functions of bacterioplankton in the Guangdong coastal zone.},
journal = {Marine life science &amp; technology},
volume = {6},
number = {3},
pages = {547-561},
pmid = {39219687},
issn = {2662-1746},
abstract = {UNLABELLED: Coastal ecosystems are an important region for biogeochemical cycling, are a hotspot of anthropogenic disturbance and play a crucial role in global carbon cycling through the metabolic activities of bacterioplankton. Bacterioplankton can be broadly classified into two lifestyles: free-living (FL) and particle-attached (PA). However, how coastal bacterioplankton the community structure, co-occurrence networks and carbon metabolic functions with different lifestyles are differentiated is still largely unknown. Understanding these processes is necessary to better determine the contributions of coastal bacterioplankton to carbon cycling. Here, the characteristics of community structure and carbon metabolism function of bacterioplankton with two lifestyles in the coastal areas of Guangdong Province were investigated using amplicon sequencing, metagenomic, and metatranscriptomic techniques. The results show that the main bacterioplankton responsible for carbon metabolism were the Pseudomonadota, Bacteroidota, and Actinomycetota. The microbial community structure, carbon metabolic function, and environmental preferences differ between different lifestyles. FL and PA bacteria exhibited higher carbon fixation and degradation potentials, respectively. A range of environmental factors, such as dissolved oxygen, pH, and temperature, were associated with the community structure and carbon metabolic functions of the bacterioplankton. Human activities, such as nutrient discharge, may affect the distribution of functional genes and enhance the carbon degradation functions of bacterioplankton. In conclusion, this study increased the understanding of the role of microorganisms in regulating carbon export in coastal ecosystems with intense human activity.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-024-00245-x.},
}
@article {pmid39218875,
year = {2024},
author = {Liwinski, T and Auer, MK and Schröder, J and Pieknik, I and Casar, C and Schwinge, D and Henze, L and Stalla, GK and Lang, UE and von Klitzing, A and Briken, P and Hildebrandt, T and Desbuleux, JC and Biedermann, SV and Holterhus, PM and Bang, C and Schramm, C and Fuss, J},
title = {Gender-affirming hormonal therapy induces a gender-concordant fecal metagenome transition in transgender individuals.},
journal = {BMC medicine},
volume = {22},
number = {1},
pages = {346},
pmid = {39218875},
issn = {1741-7015},
mesh = {Adult ; Female ; Humans ; Male ; Middle Aged ; Young Adult ; *Feces/microbiology ; *Gastrointestinal Microbiome/drug effects/genetics ; Metagenome ; Prospective Studies ; *Transgender Persons ; Sex Reassignment Procedures/methods ; Gonadal Steroid Hormones/administration &amp; dosage ; },
abstract = {BACKGROUND: Limited data exists regarding gender-specific microbial alterations during gender-affirming hormonal therapy (GAHT) in transgender individuals. This study aimed to investigate the nuanced impact of sex steroids on gut microbiota taxonomy and function, addressing this gap. We prospectively analyzed gut metagenome changes associated with 12 weeks of GAHT in trans women and trans men, examining both taxonomic and functional shifts.<br><br>METHODS: Thirty-six transgender individuals (17 trans women, 19 trans men) provided pre- and post-GAHT stool samples. Shotgun metagenomic sequencing was used to assess the changes in gut microbiota structure and potential function following GAHT.<br><br>RESULTS: While alpha and beta diversity remained unchanged during transition, specific species, including Parabacteroides goldsteinii and Escherichia coli, exhibited significant abundance shifts aligned with affirmed gender. Overall functional metagenome analysis showed a statistically significant effect of gender and transition (R[2]&#x2009;=&#x2009;4.1%, P&#x2009;=&#x2009;0.0115), emphasizing transitions aligned with affirmed gender, particularly in fatty acid-related metabolism.<br><br>CONCLUSIONS: This study provides compelling evidence of distinct taxonomic and functional profiles in the gut microbiota between trans men and women. GAHT induces androgenization in trans men and feminization in trans women, potentially impacting physiological and health-related outcomes.<br><br>TRIAL REGISTRATION: Clinicaltrials.gov NCT02185274.},
}
@article {pmid39218360,
year = {2024},
author = {Park, DG and Kang, W and Shin, IJ and Chalita, M and Oh, HS and Hyun, DW and Kim, H and Chun, J and An, YS and Lee, EJ and Yoon, JH},
title = {Difference in gut microbial dysbiotic patterns between body-first and brain-first Parkinson's disease.},
journal = {Neurobiology of disease},
volume = {201},
number = {},
pages = {106655},
doi = {10.1016/j.nbd.2024.106655},
pmid = {39218360},
issn = {1095-953X},
abstract = {BACKGROUND: This study aims to identify distinct microbial and functional biomarkers characteristic of body-first or brain-first subtypes of Parkinson's disease (PD). This could illuminate the unique pathogenic mechanisms within these subtypes.<br><br>METHODS: In this cross-sectional study, we classified 36 well-characterized PD patients into body-first, brain-first, or undetermined subtypes based on the presence of premotor REM sleep behavior disorder (RBD) and cardiac meta-iodobenzylguanidine (MIBG) uptake. We then conducted an in-depth shotgun metagenomic analysis of the gut microbiome for each subtype and compared the results with those from age- and sex-matched healthy controls.<br><br>RESULTS: Significant differences were found in the gut microbiome of body-first PD patients (n&#xa0;=&#xa0;15) compared to both brain-first PD patients (n&#xa0;=&#xa0;9) and healthy controls. The gut microbiome in body-first PD showed a distinct profile, characterized by an increased presence of Escherichia coli and Akkermansia muciniphila, and a decreased abundance of short-chain fatty acid-producing commensal bacteria. These shifts were accompanied by a higher abundance of microbial genes associated with curli protein biosynthesis and a lower abundance of genes involved in putrescine and spermidine biosynthesis. Furthermore, the combined use of premotor RBD and MIBG criteria was more strongly correlated with these microbiome differences than the use of each criterion independently.<br><br>CONCLUSIONS: Our findings highlight the significant role of dysbiotic and pathogenic gut microbial alterations in body-first PD, supporting the body-first versus brain-first hypothesis. These insights not only reinforce the gut microbiome's potential as a therapeutic target in PD but also suggest the possibility of developing subtype-specific treatment strategies.},
}
@article {pmid39218260,
year = {2024},
author = {Tang, M and Du, R and Han, X and Peng, Y},
title = {Enhancing collaboration of anammox with heterotrophic microbes mediated selectively by iron of different valences: Activities balance, metabolic mechanism, and functional genes regulation.},
journal = {Chemosphere},
volume = {364},
number = {},
pages = {143226},
doi = {10.1016/j.chemosphere.2024.143226},
pmid = {39218260},
issn = {1879-1298},
abstract = {The partial denitrification/anammox (PD/A) process is receiving increasing attention due to its cost-effectiveness advantages. However, effective strategies to alleviate organic matter inhibition and promote anammox activity have been proven to be a big challenge. This study investigated the effects of three types of iron (nano zero-valent iron (nZVI), Fe(II), and Fe(III)) on the PD/A process. It is worth noting that nZVI of 5-50 mg/L and Fe(III) of 5-120 mg/L promoted both PD and anammox activity. Long-term intermittent addition of nZVI (50 mg/L) resulted in a nitrogen removal efficiency of 98.2% in the mixotrophic PD/A system driven by iron and organic matter. The contribution of anammox for nitrogen removal reached as high as 93.8%. The organic carbon demand decreased due to the external electron donor provided by nZVI for PD. Multiple Fe-N metabolic pathways, primarily involving ammonia oxidation by Fe(III) and nitrate reduction by nZVI, play a crucial role in facilitating nitrogen transformation. Conversely, the direct addition of 30-120 mg/L Fe (II) resulted in a significant decrease in pH to below 5.0 and severe inhibition of PD and anammox activity. Following prolonged operation in the presence of nZVI, it was demonstrated that there is an enhancing effect on robust nitrite production for anammox. This was accompanied by a remarkable up-regulation of genes encoding nitrate reductase and iron-transporting proteins dominated by Thauera. Overall, this study has provided an efficient approach for advanced nitrogen removal through organic- and iron-driven anammox processes.},
}
@article {pmid39217893,
year = {2024},
author = {Wang, J and Ou, Y and Li, R and Tao, C and Liu, H and Li, R and Shen, Z and Shen, Q},
title = {The occurrence of banana Fusarium wilt aggravates antibiotic resistance genes dissemination in soil.},
journal = {Ecotoxicology and environmental safety},
volume = {283},
number = {},
pages = {116982},
doi = {10.1016/j.ecoenv.2024.116982},
pmid = {39217893},
issn = {1090-2414},
mesh = {*Musa/microbiology ; *Soil Microbiology ; *Fusarium/genetics ; *Drug Resistance, Microbial/genetics ; Plant Diseases/microbiology ; Soil/chemistry ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The spread of antibiotic resistance genes (ARGs) and subsequent soil-borne disease outbreaks are major threats to soil health and sustainable crop production. However, the relationship between occurrences of soil-borne diseases and the transmission of soil ARGs remains unclear. Here, soil ARGs, mobile genetic elements and microbial communities from co-located disease suppressive and conducive banana orchards were deciphered using metagenomics and metatranscriptomics approaches. In total, 23 ARG types, with 399 subtypes, were detected using a metagenomics approach, whereas 23 ARG types, with 452 subtypes, were discovered using a metatranscriptomics method. Furthermore, the metagenomics analysis revealed that the ARG total abundance levels were greater in rhizospheres (0.45 ARGs/16S rRNA on average) compared with bulk (0.32 ARGs/16S rRNA on average) soils. Interestingly, metatranscriptomics revealed that the total ARG abundances were greater in disease-conducive (8.85 ARGs/16S rRNA on average) soils than disease suppressive (1.45 ARGs/16S rRNA on average) soils. Mobile genetic elements showed the same trends as ARGs. Network and binning analyses indicated that Mycobacterium, Streptomyces, and Blastomonas are the main potential hosts of ARGs. Furthermore, Bacillus was significantly and negatively correlated with Fusarium (P < 0.05, r = -0.84) and hosts of ARGs (i.e., Mycobacterium, Streptomyces, and Blastomonas). By comparing metagenomic and metatranscriptomic analyses，this study demonstrated that metatranscriptomics may be more sensitive in indicating ARGs activities in soil. Our findings enable the more accurate assessment of the transmission risk of ARGs. The data provide a new perspective for recognizing soil health, in which soil-borne disease outbreaks appear to be associated with ARG spread, whereas beneficial microbe enrichment may mitigate wilt disease and ARG transmission.},
}
@article {pmid39217664,
year = {2024},
author = {Yu, Y and Wei, R and Yi, S and Teng, Y and Ning, R and Wei, S and Bai, L and Liu, H and Li, L and Xu, H and Han, C},
title = {Research Note: Integrative analysis of transcriptome and gut microbiome reveals foie gras capacity difference between cage and floor rearing systems.},
journal = {Poultry science},
volume = {103},
number = {11},
pages = {104248},
pmid = {39217664},
issn = {1525-3171},
abstract = {To explore the differences in foie gras performance between geese raised in cages and on the ground, we conducted an integrative analysis of liver transcriptome and gut microbial metagenomes. The results showed extremely significant differences in the liver weight (P < 0.01) and liver lipid accumulation of FRS and CRS groups. The levels of triglyceride (TG), high-density lipoprotein cholesterol (HDL-C) and low-density lipoprotein cholesterol (LDL-C) of CRS were significantly higher than those of FRS (P < 0.05). Transcriptome analysis showed that 3,917 upregulated and 1,395 downregulated genes were identified, and lipid metabolism pathway and fatty acid metabolism were significantly enriched. Analysis of cecum microbiota revealed that several inflammation-related bacteria (including Gallibacterium, Escherichia-Shigella, Desulfovibrio, Alistipes, and Fournierella) were enriched in CRS, while beneficial bacteria (including Lactobacillus, Limosilactobacillus, and Ligilactobacillus) were significantly enriched in FRS. In conclusion, CRS was better than FRS in foie gras production, which was more conducive to lipid deposition in the goose liver.},
}
@article {pmid39217640,
year = {2024},
author = {Shi, Y and Ji, B and Li, A and Zhang, X and Liu, Y},
title = {Enhancing the performance of microalgal-bacterial systems with sodium bicarbonate: A step forward to carbon neutrality of municipal wastewater treatment.},
journal = {Water research},
volume = {266},
number = {},
pages = {122345},
doi = {10.1016/j.watres.2024.122345},
pmid = {39217640},
issn = {1879-2448},
abstract = {The microalgal-bacterial granular sludge (MBGS) process, enhanced with sodium bicarbonate (NaHCO3), offers a sustainable alternative for wastewater treatment aiming for carbon neutrality. This study demonstrates that NaHCO3, which can be derived from the flue gases and alkaline textile wastewater, significantly enhances pollutant removal and biomass production. Optimal addition of NaHCO3 was found to achieve an inorganic-to-organic carbon ratio of 1.0 and a total carbon-to-nitrogen ratio of 5.0. Metagenomic analysis and structural equation modeling showed that NaHCO3 addition increased dissolved oxygen concentrations and pH levels, creating a more favorable environment for key microbial communities, including Proteobacteria, Chloroflexi, and Cyanobacteria. Confocal laser scanning microscopy further confirmed enhanced interactions between Cyanobacteria and Proteobacteria/Chloroflexi, facilitating the MBGS process. These microbes harbored functional genes (gap2, GLU, and ppk) critical for removing organics, nitrogen, and phosphorus. Carbon footprint analysis revealed significant reductions in CO2 emissions by the NaHCO3-added MBGS process in representative countries (China, Australia, Canada, Germany, and Morocco), compared to the conventional activated sludge process. These findings highlight the effectiveness of NaHCO3 in optimizing MBGS process, establishing it as a key strategy in achieving carbon-neutral wastewater treatment globally.},
}
@article {pmid39217389,
year = {2024},
author = {Zhang, Y and Cheng, TY and Liu, GH and Liu, L and Duan, DY},
title = {Metagenome reveals the midgut microbial community of Haemaphysalis qinghaiensis ticks collected from yaks and Tibetan sheep.},
journal = {Parasites &amp; vectors},
volume = {17},
number = {1},
pages = {370},
pmid = {39217389},
issn = {1756-3305},
support = {No. 31902294//the National Natural Science Foundation of China/ ; },
mesh = {Animals ; Sheep ; Cattle ; Female ; *Metagenome ; *Ixodidae/microbiology ; Gastrointestinal Microbiome ; Bacteria/classification/isolation &amp; purification/genetics ; Tick Infestations/veterinary/parasitology ; Sheep Diseases/microbiology/parasitology ; China ; Metagenomics ; Tibet ; Cattle Diseases/microbiology/parasitology ; },
abstract = {BACKGROUND: Haemaphysalis qinghaiensis is a tick species distributed only in China. Due to its ability to transmit a variety of pathogens, including species of the genera Anaplasma, Rickettsia, Babesia, and Theileria, it seriously endangers livestock husbandry. However, the microbial community of the midgut of H. qinghaiensis females collected from yaks and Tibetan sheep has not yet been characterized using metagenomic sequencing technology.<br><br>METHODS: Haemaphysalis qinghaiensis were collected from the skins of yaks and Tibetan sheep in Gansu Province, China. Genomic DNA was extracted from the midguts and midgut contents of fully engorged H. qinghaiensis females collected from the two hosts. Metagenomic sequencing technology was used to analyze the microbial community of the two groups.<br><br>RESULTS: Fifty-seven phyla, 483 genera, and 755 species were identified in the two groups of samples. The ticks from the two hosts harbored common and unique microorganisms. At the phylum level, the dominant common phyla were Proteobacteria, Firmicutes, and Mucoromycota. At the genus level, the dominant common genera were Anaplasma, Ehrlichia, and Pseudomonas. At the species level, bacteria including Anaplasma phagocytophilum, Ehrlichia minasensis, and Pseudomonas aeruginosa along with eukaryotes such as Synchytrium endobioticum and Rhizophagus irregularis, and viruses such as the orf virus, Alphadintovirus mayetiola, and Parasteatoda house spider adintovirus were detected in both groups. In addition, the midgut of H. qinghaiensis collected from yaks had unique microbial taxa including two phyla, eight genera, and 23 species. Unique microorganisms in the midgut of H. qinghaiensis collected from Tibetan sheep included two phyla, 14 genera, and 32 species. Kyoto Encyclopedia of Genes and Genomes enrichment analysis revealed that the functional genes of the microbiome of H. qinghaiensis were annotated to six pathways, and the metabolic pathways included 11 metabolic processes, in which the genes involved in carbohydrate metabolism were the most abundant, followed by the genes involved in lipid metabolism.<br><br>CONCLUSIONS: These findings indicate that most of the microbial species in the collected H. qinghaiensis ticks were the same in both hosts, but there were also slight differences. The analytical data from this study have enhanced our understanding of the midgut microbial composition of H. qinghaiensis collected from different hosts. The database of H. qinghaiensis microbe constructed from this study will lay the foundation for predicting tick-borne diseases. Furthermore, a comprehensive understanding of tick microbiomes will be useful for understanding vector competency and interactions with ticks and midgut microorganisms.},
}
@article {pmid39217229,
year = {2024},
author = {Gyaltshen, Y and Ishii, Y and Charvet, S and Goetz, E and Maruyama, S and Kim, E},
title = {Molecular diversity of green-colored microbial mats from hot springs of northern Japan.},
journal = {Extremophiles : life under extreme conditions},
volume = {28},
number = {3},
pages = {43},
pmid = {39217229},
issn = {1433-4909},
support = {KAKENHI 17H05713//Japan Society for the Promotion of Science/ ; 19H04713//Japan Society for the Promotion of Science/ ; CAREER 1453639//Division of Integrative Organismal Systems/ ; },
mesh = {*Hot Springs/microbiology ; Japan ; RNA, Ribosomal, 16S/genetics ; Metagenome ; Microbiota ; Bacteria/genetics/classification/isolation &amp; purification ; Phylogeny ; },
abstract = {We acquired and analyzed metagenome and 16S/18S rRNA gene amplicon data of green-colored microbial mats from two hot springs within the Onikobe geothermal region (Miyagi Prefecture, Japan). The two collection sites-Tamago and Warabi-were in proximity and had the same temperature (40 °C), but the Tamago site was connected to a nearby stream, whereas the Warabi site was isolated. Both the amplicon and metagenome data suggest the bacterial, especially cyanobacterial, dominance of the mats; other abundant groups include Chloroflexota, Pseudomonadota, Bacteroidota/Chlorobiota, and Deinococcota. At finer resolution, however, the taxonomic composition entirely differed between the mats. A total of 5 and 21 abundant bacterial 16S rRNA gene OTUs were identified for Tamago and Warabi, respectively; of these, 12 are putative chlorophyll- or rhodopsin-based phototrophs. The presence of phylogenetically diverse microbial eukaryotes was noted, with ciliates and amoebozoans being the most abundant eukaryote groups for Tamago and Warabi, respectively. Fifteen metagenome-assembled genomes (MAGs) were obtained, represented by 13 bacteria, one ciliate (mitochondrion), and one giant virus. A total of 15 novel taxa, including a new deeply branching Chlorobiota species, is noted from the amplicon and MAG data, highlighting the importance of environmental sequencing in uncovering hidden microorganisms.},
}
@article {pmid39216995,
year = {2024},
author = {Gekenidis, MT and Vollenweider, V and Joyce, A and Murphy, S and Walser, JC and Ju, F and Bürgmann, H and Hummerjohann, J and Walsh, F and Drissner, D},
title = {Unde venis? Bacterial resistance from environmental reservoirs to lettuce: tracking microbiome and resistome over a growth period.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiae118},
pmid = {39216995},
issn = {1574-6941},
abstract = {Fresh produce is suggested to contribute highly to shaping the gut resistome. We investigated the impact of pig manure and irrigation water quality on microbiome and resistome of field-grown lettuce over an entire growth period. Lettuce was grown under four regimes, combining soil amendment with manure (with/without) with sprinkler irrigation using river water with an upstream wastewater input, disinfected by UV (with/without). Lettuce leaves, soil, and water samples were collected weekly and analyzed by bacterial cultivation, 16S rRNA gene amplicon sequencing, and shotgun metagenomics from total community DNA. Cultivation yielded only few clinically relevant antibiotic-resistant bacteria (ARB), but numbers of ARB on lettuce increased over time, while no treatment-dependent changes were observed. Microbiome analysis confirmed a temporal trend. Antibiotic resistance genes (ARGs) unique to lettuce and water included multidrug and β-lactam ARGs, whereas lettuce and soil uniquely shared mainly glycopeptide and tetracycline ARGs. Surface water carried clinically relevant ARB (e.g. ESBL-producing Escherichia coli or Serratia fonticola) without affecting the overall lettuce resistome significantly. Resistance markers including biocide and metal resistance were increased in lettuce grown with manure, especially young lettuce (increased soil contact). Overall, while all investigated environments had their share as sources of the lettuce resistome, manure was the main source especially on young plants. We therefore suggest minimizing soil-vegetable contact to minimize resistance markers on fresh produce.},
}
@article {pmid39216705,
year = {2024},
author = {Li, Y and Chen, Y and Kang, L and Cao, Z and Lv, J and Wang, S and Guo, C and Wang, J},
title = {Metagenomic analysis reveals enhanced sludge dewaterability through acidified sludge inoculation: Regulation of Fe (II) oxidation electron transport pathway.},
journal = {Bioresource technology},
volume = {412},
number = {},
pages = {131367},
doi = {10.1016/j.biortech.2024.131367},
pmid = {39216705},
issn = {1873-2976},
mesh = {*Sewage/microbiology ; *Oxidation-Reduction ; *Metagenomics/methods ; Electron Transport ; Ferrous Compounds/metabolism ; Iron/metabolism ; Water/chemistry ; },
abstract = {The bioleaching utilizing indigenous microbial inoculation can continuously improve the dewaterability of sludge. In this study, metagenomic analysis was innovative employed to identify the key microorganisms and functional genes that affect the dewatering performance of sludge in the bioleaching conditioning process. The results demonstrated that long-term repeated inoculation of acidified sludge resulted in increased abundance of many functional genes associated with the transport of carbohydrate and amino acid. Additionally, genes encoding key iron transport proteins (such as afuA, fhuC, and fhuD) and genes related to electron transfer carriers in ferrous iron oxidation process (such as rus and cyc2) were significantly enriched, thereby promoting the improvement of sludge dewatering performance through enhanced iron oxidation. Notably, Acidithiobacillus, Betaproteobacteria, and Hyphomicrobium were the major sources of functional genes. This study reveals the microscopic mechanisms underlying the improvement of sludge dewaterability through bioleaching based on mixed culture from a novel perspective of gene metabolism.},
}
@article {pmid39216617,
year = {2024},
author = {Borrego, A and Koury Cabrera, WH and Souza, AT and Eto, SF and de Oliveira, SL and Rodrigues, J and Jensen, JR},
title = {Microbiota transfer early after birth modulates genetic susceptibility to chronic arthritis in mice.},
journal = {Microbes and infection},
volume = {},
number = {},
pages = {105411},
doi = {10.1016/j.micinf.2024.105411},
pmid = {39216617},
issn = {1769-714X},
abstract = {Genetics is central to the susceptibility or resistance to autoimmunity, and mounting evidence indicates that the intestinal microbiota also plays an essential role. In murine arthritis models, short-chain fat acid supplementation reduces disease severity by modulating tryptophan-metabolizing bacteria. Common microbiota transfer methods modulate arthritis severity, however, they are not practical for chronic models such as pristane-induced arthritis (PIA). PIA-resistant (HIII) and PIA-susceptible (LIII) mice harbor diverse intestinal microbiomes, which might be implicated in their divergent susceptibility. To investigate this hypothesis, we used cross-fostering to stably transfer the microbiota. In this study, we show that extreme susceptibility to arthritis can be modulated by early microbiota transfer, with long-lasting effects. HIII and LIII pups were cross-fostered and injected with pristane after weaning. PIA severity in cross-fostered LIII mice was significantly reduced in the chronic phase. Metagenomic analyses showed that HIII and LIII microbiomes were partly shifted by cross-fostering. Microbial groups whose abundance was associated with either HIII or LIII mice presented similar composition in cross-fostered mice of the opposite strains, suggesting a role in PIA susceptibility. Identification of bacterial groups that modulate chronic arthritis will contribute novel insights on the pathogenesis of human rheumatoid arthritis and targets for replication and functional studies.},
}
@article {pmid39216430,
year = {2024},
author = {Gupta, A and Shivachandran, A and Saleena, LM},
title = {Oral microbiome insights: Tracing acidic culprits in dental caries with functional metagenomics.},
journal = {Archives of oral biology},
volume = {168},
number = {},
pages = {106064},
doi = {10.1016/j.archoralbio.2024.106064},
pmid = {39216430},
issn = {1879-1506},
mesh = {*Dental Caries/microbiology ; Humans ; *Metagenomics/methods ; *Microbiota ; Mouth/microbiology ; Acids/metabolism ; Bacteria/classification/genetics ; DNA, Bacterial ; Sequence Analysis, DNA ; Male ; Female ; },
abstract = {OBJECTIVE: This study aimed to investigate the presence and abundance of acid-producing bacteria in dental caries samples using functional gene prediction techniques.<br><br>DESIGN: A total of 24 dental caries samples were collected for analysis. DNA isolation was performed followed by shotgun metagenomic sequencing. Functional gene prediction techniques were used to identify enzymes responsible for acid production from primary metabolites. Enzymes responsible for converting primary metabolites into acids were identified from the KEGG database. Subsequently, 840 contigs were examined, and their genus and species were characterized.<br><br>RESULTS: Analysis of the obtained data revealed 31 KEGG IDs corresponding to enzymes involved in the conversion of primary metabolites into acids. All 117 identified genera from the contig analysis were found to be part of the oral microbiome. In addition, A higher prevalence of acid-producing bacteria was noted in dental caries samples compared to earlier reports.<br><br>CONCLUSION: The study indicates the significant role of acid-producing bacteria in the initiation and progression of dental caries. The findings highlight the importance of microbial activity in the demineralization process of tooth enamel. Methods for preventing dental decay may be promising if specific measures are implemented to reduce the amount of acid produced by oral bacteria.},
}
@article {pmid39216362,
year = {2024},
author = {Zhuang, J and Hou, Y and Wang, Y and Gao, Y and Chen, Y and Qi, J and Li, P and Bian, Y and Ju, N},
title = {Relationship between microorganisms and milk metabolites during quality changes in refrigerated raw milk: A metagenomic and metabolomic exploration.},
journal = {International journal of food microbiology},
volume = {425},
number = {},
pages = {110891},
doi = {10.1016/j.ijfoodmicro.2024.110891},
pmid = {39216362},
issn = {1879-3460},
mesh = {*Milk/microbiology ; Animals ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; *Refrigeration ; Metagenomics ; Food Storage ; Metabolomics ; Food Microbiology ; Cattle ; },
abstract = {Although cold storage at 4 °C can effectively prolong the shelf life of raw milk, it cannot prevent its eventual spoilage. In this study, we analyzed the main physicochemical and microbial indexes of raw milk stored at 4 °C for 6 days. The changes in microbial profiles and milk metabolites and their relationship during refrigeration were also explored. Metagenomic analysis performed using the Illumina Hiseq Xten sequencing platform revealed that the dominant genera in raw milk evolved from Acinetobacter, Streptococcus, Staphylococcus, and Anaplasma to Flavobacterium, Pseudomonas, and Lactococcus during cold storage. Using the UHPLC-Q-TOF MS method, 77 significantly different metabolites (p < 0.05) were identified, among which lipids were the most abundant (37). The most significant metabolic changes largely occurred at 3-4 days of refrigeration, coinciding with the rapid increase in dominant psychrotrophic bacteria. Subsequently, correlation analysis demonstrated that these lipid-related metabolites were significantly associated with Acinetobacter, Flavobacterium, and Pseudomonas. Both macro indicators and microanalysis indicated that the key stage of quality changes in raw milk was 3-4 days. Thus, this stage can be targeted for the quality control of raw milk.},
}
@article {pmid39216241,
year = {2024},
author = {Liao, X and Hou, L and Zhang, L and Grossart, HP and Liu, K and Liu, J and Chen, Y and Liu, Y and Hu, A},
title = {Distinct influences of altitude on microbiome and antibiotic resistome assembly in a glacial river ecosystem of Mount Everest.},
journal = {Journal of hazardous materials},
volume = {479},
number = {},
pages = {135675},
doi = {10.1016/j.jhazmat.2024.135675},
pmid = {39216241},
issn = {1873-3336},
mesh = {*Rivers/microbiology ; *Altitude ; *Microbiota/drug effects ; *Drug Resistance, Microbial/genetics ; Ecosystem ; Bacteria/genetics/drug effects/classification ; Geologic Sediments/microbiology ; Viruses/drug effects/genetics ; Anti-Bacterial Agents/pharmacology ; Ice Cover/microbiology ; China ; },
abstract = {The profound influences of altitude on aquatic microbiome were well documented. However, differences in the responses of different life domains (bacteria, microeukaryotes, viruses) and antibiotics resistance genes (ARGs) in glacier river ecosystems to altitude remain unknown. Here, we employed shotgun metagenomic and amplicon sequencing to characterize the altitudinal variations of microbiome and ARGs in the Rongbu River, Mount Everest. Our results indicated the relative influences of stochastic processes on microbiome and ARGs assembly in water and sediment were in the following order: microeukaryotes < ARGs < viruses < bacteria. Moreover, distinct assembly patterns of the microbiome and ARGs were found in response to differences in altitude, the latter of which shift from deterministic to stochastic processes with increasing differences in altitude. Partial least squares path modeling revealed that mobile genetic elements (MGEs) and viral β-diversity were the major factors influencing the ARG abundances. Taken together, our work revealed that altitude-caused environmental changes led to significant changes in the composition and assembly processes of the microbiome and ARGs, while ARGs had a unique response pattern to altitude. Our findings provide novel insights into the impacts of altitude on the biogeographic distribution of microbiome and ARGs, and the associated driving forces in glacier river ecosystems.},
}
@article {pmid39216231,
year = {2024},
author = {Xu, J and Li, P and Li, Z and Liu, S and Guo, H and Lesser, CF and Ke, J and Zhao, W and Mou, X},
title = {Gut bacterial type III secretion systems aggravate colitis in mice and serve as biomarkers of Crohn's disease.},
journal = {EBioMedicine},
volume = {107},
number = {},
pages = {105296},
pmid = {39216231},
issn = {2352-3964},
mesh = {Animals ; Mice ; *Crohn Disease/microbiology/metabolism/pathology ; Humans ; *Biomarkers ; *Disease Models, Animal ; *Gastrointestinal Microbiome ; *Type III Secretion Systems/metabolism/genetics ; Colitis/microbiology/metabolism ; Metagenomics/methods ; Feces/microbiology ; Female ; Male ; },
abstract = {BACKGROUND: Mesenteric adipose tissue (mAT) hyperplasia, known as creeping fat, is a pathologic characteristic of Crohn's disease (CD). In our previously reported cohort, we observed that Achromobacter pulmonis was the most abundant and prevalent bacteria cultivated from creeping fat.<br><br>METHODS: A whole genomic sequencing and identification of T3SS orthologs of mAT-derived A. pulmonis were used. A functional type III secretion system (T3SS) mediated the pathogenic potential of A. pulmonis in&#xa0;vitro and in mouse colitis model. Furthermore, a T3SS Finder pipeline was introduced to evaluate gut bacterial T3SS orthologs in the feces of CD patients, ulcerative colitis and colorectal cancer patients.<br><br>FINDINGS: Here, we reveal that mAT-derived A. pulmonis possesses a functional T3SS, aggravates colitis in mice via T3SS, and exhibits T3SS-dependent cytotoxicity via a caspase-independent mechanism in macrophages and epithelial cells, which demonstrated the pathogenic potential of the T3SS-harboring A. pulmonis. Metagenomic analyses demonstrate an increased abundance of Achromobacter in the fecal of Crohn's disease patients compared to healthy controls. A comprehensive comparison of total microbial vT3SS abundance in various intestine diseases demonstrated that the specific enrichment of vT3SS genes was shown in fecal samples of CD, neither ulcerative colitis nor colorectal cancer patients, and ten T3SS gene-based biomarkers for CD were discovered and validated in a newly recruited CD cohort. Furthermore, treatment with exclusive enteral nutrition (EEN), an intervention that improves CD patient symptomatology, was found associated with a significant reduction in the prevalence of T3SS genes in fecal samples.<br><br>INTERPRETATION: These findings highlight the pathogenic significance of T3SSs in the context of CD and identify specific T3SS genes that could potentially function as biomarkers for diagnosing and monitoring the clinical status of CD patients.<br><br>FUNDING: This work is supported by the National Key Research and Development Program of China (2020YFA0907800), the China Postdoctoral Science Foundation (2023M744089), the National Natural Science Foundation of China (32000096), the Shenzhen Science and Technology Programs (KQTD20200820145822023, RCIC20231211085944057, and ZDSYS20220606100803007), National Key Clinical Discipline, Guangdong Provincial Clinical Research Center for Digestive Diseases (2020B1111170004), Qingfeng Scientific Research Fund of the China Crohn's &amp; Colitis Foundation (CCCF) (CCCF-QF-2022B71-1), and the Sixth Affiliated Hospital, Sun Yat-sen University Clinical Research 1010 Program 1010CG(2023)-08. These funding provided well support for this research work, which involved data collection, analysis, interpretation, patient recruitment and so on.},
}
@article {pmid39216125,
year = {2024},
author = {Kim, DW and Woo, DU and Kim, UI and Kang, YJ and Koo, OK},
title = {Development of a novel crAss-like phage detection method with a broad spectrum for microbial source tracking.},
journal = {Water research},
volume = {266},
number = {},
pages = {122330},
doi = {10.1016/j.watres.2024.122330},
pmid = {39216125},
issn = {1879-2448},
abstract = {CrAssphage has been recognized as the most abundant and human-specific bacteriophage in the human gut. Consequently, crAssphage has been used as a microbial source tracking (MST) marker to monitor human fecal contamination. Many crAss-like phages (CLPs) have been recently discovered, expanding the classification into the new order Crassvirales. This study aims to assess CLP prevalence in South Korea and develop a detection system for MST applications. Thirteen CLPs were identified in six human fecal samples and categorized into seven genera via metagenomic analysis. The major head protein (MHP) displayed increased sequence similarity within each genus. Eight PCR primer candidates, designed from MHP sequences, were evaluated in animal and human feces. CLPs were absent in animal feces except for those from raccoons, which hosted genera VI, VIIa, and VIIb. CLPs were detected in 91.52% (54/59) of humans, with genus VI (38 out of 59) showing the highest prevalence, nearly double that of p-crAssphage in genus I (22 out of 59). This study highlights genus VI as a potent MST marker, broadening the detection range for CLPs. Human-specific and selectively targeted MST markers can significantly impact hygiene regulations, lowering public health costs through their application in screening liver, sewage, wastewater, and various environmental samples.},
}
@article {pmid39215755,
year = {2024},
author = {Cannarozzi, AL and Latiano, A and Massimino, L and Bossa, F and Giuliani, F and Riva, M and Ungaro, F and Guerra, M and Brina, ALD and Biscaglia, G and Tavano, F and Carparelli, S and Fiorino, G and Danese, S and Perri, F and Palmieri, O},
title = {Inflammatory bowel disease genomics, transcriptomics, proteomics and metagenomics meet artificial intelligence.},
journal = {United European gastroenterology journal},
volume = {},
number = {},
pages = {},
doi = {10.1002/ueg2.12655},
pmid = {39215755},
issn = {2050-6414},
support = {PNRR-MAD-2022-12375729//Italian Next Generation Eu Program/ ; },
abstract = {Various extrinsic and intrinsic factors such as drug exposures, antibiotic treatments, smoking, lifestyle, genetics, immune responses, and the gut microbiome characterize ulcerative colitis and Crohn's disease, collectively called inflammatory bowel disease (IBD). All these factors contribute to the complexity and heterogeneity of the disease etiology and pathogenesis leading to major challenges for the scientific community in improving management, medical treatments, genetic risk, and exposome impact. Understanding the interaction(s) among these factors and their effects on the immune system in IBD patients has prompted advances in multi-omics research, the development of new tools as part of system biology, and more recently, artificial intelligence (AI) approaches. These innovative approaches, supported by the availability of big data and large volumes of digital medical datasets, hold promise in better understanding the natural histories, predictors of disease development, severity, complications and treatment outcomes in complex diseases, providing decision support to doctors, and promising to bring us closer to the realization of the "precision medicine" paradigm. This review aims to provide an overview of current IBD omics based on both individual (genomics, transcriptomics, proteomics, metagenomics) and multi-omics levels, highlighting how AI can facilitate the integration of heterogeneous data to summarize our current understanding of the disease and to identify current gaps in knowledge to inform upcoming research in this field.},
}
@article {pmid39211485,
year = {2024},
author = {Tran, DM and Nguyen, DS and Nguyen, TH and Tran, TPH and Nguyen, AD},
title = {Shotgun metagenomic dataset of root endophytic microbiome of citrus (Citrus nobilis L.).},
journal = {Data in brief},
volume = {56},
number = {},
pages = {110777},
pmid = {39211485},
issn = {2352-3409},
abstract = {Citrus (Citrus nobilis L.) is one of the main fruit crops in Dak Lak Province of Vietnam; however, a dataset on the endophytic microbiome of this plant has yet to be discovered. This article presented the endophytic microbial dataset from roots of healthy Citrus nobilis L. collected in Dak Lak for the first time. We found that 4 kingdoms, 30 phyla, 58 classes, 125 orders, 242 families, 722 genera, and 1637 species of endophytic microorganisms were identified from the sample. Actinomycetota was shown to be the main phylum (64.36 %) and biosynthesis to be the most abundant function (55.64 %) of the endophytic microbial community. Data provided insights into the composition and functional diversity of the Citrus nobilis L. endophytic microbiome, especially novel microbial resources. They could be used for the next works towards applying the endophytic microbiome for sustainable citrus production.},
}
@article {pmid39209868,
year = {2024},
author = {Gonzalez, E and Lee, MD and Tierney, BT and Lipieta, N and Flores, P and Mishra, M and Beckett, L and Finkelstein, A and Mo, A and Walton, P and Karouia, F and Barker, R and Jansen, RJ and Green, SJ and Weging, S and Kelliher, J and Singh, NK and Bezdan, D and Galazska, J and Brereton, NJB},
title = {Spaceflight alters host-gut microbiota interactions.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {71},
pmid = {39209868},
issn = {2055-5008},
mesh = {*Gastrointestinal Microbiome ; Animals ; *Space Flight ; Mice ; *Bacteria/classification/genetics ; Liver/microbiology ; Host Microbial Interactions ; Metagenomics/methods ; Colon/microbiology ; Bile Acids and Salts/metabolism ; Energy Metabolism ; Male ; Humans ; Mice, Inbred C57BL ; },
abstract = {The ISS rodent habitat has provided crucial insights into the impact of spaceflight on mammals, inducing symptoms characteristic of liver disease, insulin resistance, osteopenia, and myopathy. Although these physiological responses can involve the microbiome on Earth, host-microbiota interactions during spaceflight are still being elucidated. We explore murine gut microbiota and host gene expression in the colon and liver after 29 and 56 days of spaceflight using multiomics. Metagenomics revealed significant changes in 44 microbiome species, including relative reductions in bile acid and butyrate metabolising bacteria like Extibacter muris and Dysosmobacter welbionis. Functional prediction indicate over-representation of fatty acid and bile acid metabolism, extracellular matrix interactions, and antibiotic resistance genes. Host gene expression described corresponding changes to bile acid and energy metabolism, and immune suppression. These changes imply that interactions at the host-gut microbiome interface contribute to spaceflight pathology and that these interactions might critically influence human health and long-duration spaceflight feasibility.},
}
@article {pmid39209853,
year = {2024},
author = {Mi, J and Jing, X and Ma, C and Yang, Y and Li, Y and Zhang, Y and Long, R and Zheng, H},
title = {Massive expansion of the pig gut virome based on global metagenomic mining.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {76},
pmid = {39209853},
issn = {2055-5008},
mesh = {Animals ; Swine ; *Virome/genetics ; *Metagenomics/methods ; *Gastrointestinal Microbiome ; *Viruses/genetics/classification/isolation &amp; purification ; *Genome, Viral ; Data Mining ; Metagenome ; Phylogeny ; },
abstract = {The pig gut virome plays a vital role in the gut microbial ecosystem of pigs. However, a comprehensive understanding of their diversity and a reference database for the virome are currently lacking. To address this gap, we established a Pig Virome Database (PVD) that comprised of 5,566,804 viral contig sequences from 4650 publicly available gut metagenomic samples using a pipeline designated "metav". By clustering sequences, we identified 48,299 viral operational taxonomic units (vOTUs) genomes of at least medium quality, of which 92.83% of which were not found in existing major databases. The majority of vOTUs were identified as Caudoviricetes (72.21%). The PVD database contained a total of 2,362,631 protein-coding genes across the above medium-quality vOTUs genomes that can be used to explore the functional potential of the pig gut virome. These findings highlight the extensive diversity of viruses in the pig gut and provide a pivotal reference dataset for forthcoming research concerning the pig gut virome.},
}
@article {pmid39209850,
year = {2024},
author = {Colman, DR and Keller, LM and Arteaga-Pozo, E and Andrade-Barahona, E and St Clair, B and Shoemaker, A and Cox, A and Boyd, ES},
title = {Covariation of hot spring geochemistry with microbial genomic diversity, function, and evolution.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {7506},
pmid = {39209850},
issn = {2041-1723},
support = {80NSSC19M0150//National Aeronautics and Space Administration (NASA)/ ; 80NSSC19M0150//National Aeronautics and Space Administration (NASA)/ ; 80NSSC19M0150//National Aeronautics and Space Administration (NASA)/ ; 4069947046//National Aeronautics and Space Administration (NASA)/ ; 4069947046//National Aeronautics and Space Administration (NASA)/ ; 4069947046//National Aeronautics and Space Administration (NASA)/ ; 4069947046//National Aeronautics and Space Administration (NASA)/ ; },
mesh = {*Hot Springs/microbiology/chemistry ; *Metagenome ; *Phylogeny ; Bacteria/genetics/classification/metabolism ; Hydrogen-Ion Concentration ; Archaea/genetics/classification/metabolism ; Genome, Microbial ; Ecosystem ; Microbiota/genetics ; },
abstract = {The geosphere and the microbial biosphere have co-evolved for ~3.8 Ga, with many lines of evidence suggesting a hydrothermal habitat for life's origin. However, the extent that contemporary thermophiles and their hydrothermal habitats reflect those that likely existed on early Earth remains unknown. To address this knowledge gap, 64 geochemical analytes were measured and 1022 metagenome-assembled-genomes (MAGs) were generated from 34 chemosynthetic high-temperature springs in Yellowstone National Park and analysed alongside 444 MAGs from 35 published metagenomes. We used these data to evaluate co-variation in MAG taxonomy, metabolism, and phylogeny as a function of hot spring geochemistry. We found that cohorts of MAGs and their functions are discretely distributed across pH gradients that reflect different geochemical provinces. Acidic or circumneutral/alkaline springs harbor MAGs that branched later and are enriched in sulfur- and arsenic-based O2-dependent metabolic pathways that are inconsistent with early Earth conditions. In contrast, moderately acidic springs sourced by volcanic gas harbor earlier-branching MAGs that are enriched in anaerobic, gas-dependent metabolisms (e.g. H2, CO2, CH4 metabolism) that have been hypothesized to support early microbial life. Our results provide insight into the influence of redox state in the eco-evolutionary feedbacks between thermophiles and their habitats and suggest moderately acidic springs as early Earth analogs.},
}
@article {pmid39215001,
year = {2024},
author = {Becsei, &#xc1; and Fuschi, A and Otani, S and Kant, R and Weinstein, I and Alba, P and Stéger, J and Visontai, D and Brinch, C and de Graaf, M and Schapendonk, CME and Battisti, A and De Cesare, A and Oliveri, C and Troja, F and Sironen, T and Vapalahti, O and Pasquali, F and Bányai, K and Makó, M and Pollner, P and Merlotti, A and Koopmans, M and Csabai, I and Remondini, D and Aarestrup, FM and Munk, P},
title = {Time-series sewage metagenomics distinguishes seasonal, human-derived and environmental microbial communities potentially allowing source-attributed surveillance.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {7551},
pmid = {39215001},
issn = {2041-1723},
support = {NNF16OC0021856//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF16OC0021856//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; 874735//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 874735//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; },
mesh = {*Sewage/microbiology ; *Metagenomics/methods ; *Seasons ; Humans ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation &amp; purification ; *Metagenome/genetics ; Europe ; },
abstract = {Sewage metagenomics has risen to prominence in urban population surveillance of pathogens and antimicrobial resistance (AMR). Unknown species with similarity to known genomes cause database bias in reference-based metagenomics. To improve surveillance, we seek to recover sewage genomes and develop a quantification and correlation workflow for these genomes and AMR over time. We use longitudinal sewage sampling in seven treatment plants from five major European cities to explore the utility of catch-all sequencing of these population-level samples. Using metagenomic assembly methods, we recover 2332 metagenome-assembled genomes (MAGs) from prokaryotic species, 1334 of which were previously undescribed. These genomes account for ~69% of sequenced DNA and provide insight into sewage microbial dynamics. Rotterdam (Netherlands) and Copenhagen (Denmark) show strong seasonal microbial community shifts, while Bologna, Rome, (Italy) and Budapest (Hungary) have occasional blooms of Pseudomonas-dominated communities, accounting for up to ~95% of sample DNA. Seasonal shifts and blooms present challenges for effective sewage surveillance. We find that bacteria of known shared origin, like human gut microbiota, form communities, suggesting the potential for source-attributing novel species and their ARGs through network community analysis. This could significantly improve AMR tracking in urban environments.},
}
@article {pmid39214983,
year = {2024},
author = {Duan, Y and Santos-Júnior, CD and Schmidt, TS and Fullam, A and de Almeida, BLS and Zhu, C and Kuhn, M and Zhao, XM and Bork, P and Coelho, LP},
title = {A catalog of small proteins from the global microbiome.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {7563},
pmid = {39214983},
issn = {2041-1723},
support = {61932008//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Microbiota/genetics ; *Open Reading Frames/genetics ; *Bacteria/genetics/classification/metabolism ; *Metagenome/genetics ; *Archaea/genetics/metabolism/classification ; Molecular Sequence Annotation ; Bacterial Proteins/genetics/metabolism ; },
abstract = {Small open reading frames (smORFs) shorter than 100 codons are widespread and perform essential roles in microorganisms, where they encode proteins active in several cell functions, including signal pathways, stress response, and antibacterial activities. However, the ecology, distribution and role of small proteins in the global microbiome remain unknown. Here, we construct a global microbial smORFs catalog (GMSC) derived from 63,410 publicly available metagenomes across 75 distinct habitats and 87,920 high-quality isolate genomes. GMSC contains 965 million non-redundant smORFs with comprehensive annotations. We find that archaea harbor more smORFs proportionally than bacteria. We moreover provide a tool called GMSC-mapper to identify and annotate small proteins from microbial (meta)genomes. Overall, this publicly-available resource demonstrates the immense and underexplored diversity of small proteins.},
}
@article {pmid39214976,
year = {2024},
author = {Yi, X and Liang, JL and Wen, P and Jia, P and Feng, SW and Liu, SY and Zhuang, YY and Guo, YQ and Lu, JL and Zhong, SJ and Liao, B and Wang, Z and Shu, WS and Li, JT},
title = {Giant viruses as reservoirs of antibiotic resistance genes.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {7536},
pmid = {39214976},
issn = {2041-1723},
mesh = {*Phylogeny ; *Giant Viruses/genetics ; *Genome, Viral/genetics ; Drug Resistance, Microbial/genetics ; Bacteriophages/genetics/isolation &amp; purification ; Anti-Bacterial Agents/pharmacology ; Metagenome/genetics ; Gene Transfer, Horizontal ; Trimethoprim/pharmacology ; Drug Resistance, Bacterial/genetics ; },
abstract = {Nucleocytoplasmic large DNA viruses (NCLDVs; also called giant viruses), constituting the phylum Nucleocytoviricota, can infect a wide range of eukaryotes and exchange genetic material with not only their hosts but also prokaryotes and phages. A few NCLDVs were reported to encode genes conferring resistance to beta‑lactam, trimethoprim, or pyrimethamine, suggesting that they are potential vehicles for the transmission of antibiotic resistance genes (ARGs) in the biome. However, the incidence of ARGs across the phylum Nucleocytoviricota, their evolutionary characteristics, their dissemination potential, and their association with virulence factors remain unexplored. Here, we systematically investigated ARGs of 1416 NCLDV genomes including those of almost all currently available cultured isolates and high-quality metagenome-assembled genomes from diverse habitats across the globe. We reveal that 39.5% of them carry ARGs, which is approximately 37 times higher than that for phage genomes. A total of 12 ARG types are encoded by NCLDVs. Phylogenies of the three most abundant NCLDV-encoded ARGs hint that NCLDVs acquire ARGs from not only eukaryotes but also prokaryotes and phages. Two NCLDV-encoded trimethoprim resistance genes are demonstrated to confer trimethoprim resistance in Escherichia coli. The presence of ARGs in NCLDV genomes is significantly correlated with mobile genetic elements and virulence factors.},
}
@article {pmid39214237,
year = {2024},
author = {Macowan, M and Pattaroni, C and Bonner, K and Chatzis, R and Daunt, C and Gore, M and Custovic, A and Shields, MD and Power, UF and Grigg, J and Roberts, G and Ghazal, P and Schwarze, J and Turner, S and Bush, A and Saglani, S and Lloyd, CM and Marsland, BJ},
title = {Deep Multi-Omic Profiling Reveals Molecular Signatures that Underpin Preschool Wheeze and Asthma.},
journal = {The Journal of allergy and clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaci.2024.08.017},
pmid = {39214237},
issn = {1097-6825},
abstract = {BACKGROUND: Wheezing in childhood is prevalent, with over half of all children experiencing at least one episode by age six. The pathophysiology of wheeze, especially why some children develop asthma while others do not, remains unclear.<br><br>OBJECTIVE: This study addresses the knowledge gap by investigating the transition from preschool wheeze to asthma using multi-omic profiling.<br><br>METHODS: Unsupervised, group-agnostic integrative multi-omic factor analysis was performed using host/bacterial (meta-)transcriptomic and bacterial shotgun metagenomic datasets from bronchial brush samples paired with metabolomic/lipidomic data from bronchoalveolar lavage samples acquired from children 1-17 years old.<br><br>RESULTS: Two multi-omic factors were identified: one characterising preschool-aged recurrent wheeze and another capturing an inferred trajectory from health to wheeze and school-aged asthma. Recurrent wheeze was driven by Type 1-immune signatures, coupled with upregulation of immune-related and neutrophil-associated lipids and metabolites. Comparatively, progression towards asthma from ages 1-18 was dominated by changes related to airway epithelial cell gene expression, Type 2-immune responses, and constituents of the airway microbiome, such as increased Haemophilus influenzae.<br><br>CONCLUSION: These factors highlighted distinctions between an inflammation-related phenotype in preschool wheeze, and the predominance of airway epithelial-related changes linked with the inferred trajectory toward asthma. These findings provide insights into the differential mechanisms driving the progression from wheeze to asthma and may inform targeted therapeutic strategies.},
}
@article {pmid39214173,
year = {2024},
author = {Pan, K and Qian, Z and Guo, T and Chen, Y and Li, F and Ding, M and Ma, X and Li, J},
title = {Effects of iron-carbon on nitrogen metabolism of floc and aerobic granular sludge.},
journal = {Bioresource technology},
volume = {413},
number = {},
pages = {131376},
doi = {10.1016/j.biortech.2024.131376},
pmid = {39214173},
issn = {1873-2976},
abstract = {The aerobic granular sludge (AGS) process had been extensively studied for its simultaneous nitrification and denitrification (SND) capabilities. Iron-carbon (IC) had enhanced AGS nitrogen removal efficiency, but the mechanism remained unclear. In this study, four reactors had been added with 50, 30, 10, and 0 g/L of IC. Total nitrogen removal efficiency increased with IC dosage under the same operation mode. IC enhanced sludge ammonia oxidation rate, denitrification rate, and specific oxygen uptake rate, allowing SND to complete 60 min earlier, potentially reducing wastewater treatment costs. Notably, IC eliminated nitrite accumulation in conventional AGS effluent. IC decreased the abundance of genes and enzyme activities related to NOR expression, while increasing those related to NOS, which may mitigate the potential for nitrous oxide formation by microorganisms. In this study, IC acted as an enzymatic reaction activator, affecting granules more than flocs, with the activity gap gradually decreasing with the IC dosage.},
}
@article {pmid39214080,
year = {2024},
author = {Carlino, N and Blanco-Míguez, A and Punčochář, M and Mengoni, C and Pinto, F and Tatti, A and Manghi, P and Armanini, F and Avagliano, M and Barcenilla, C and Breselge, S and Cabrera-Rubio, R and Calvete-Torre, I and Coakley, M and Cobo-Díaz, JF and De Filippis, F and Dey, H and Leech, J and Klaassens, ES and Knobloch, S and O'Neil, D and Quijada, NM and Sabater, C and Skírnisdóttir, S and Valentino, V and Walsh, L and , and Alvarez-Ordóñez, A and Asnicar, F and Fackelmann, G and Heidrich, V and Margolles, A and Marteinsson, VT and Rota Stabelli, O and Wagner, M and Ercolini, D and Cotter, PD and Segata, N and Pasolli, E},
title = {Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2024.07.039},
pmid = {39214080},
issn = {1097-4172},
abstract = {Complex microbiomes are part of the food we eat and influence our own microbiome, but their diversity remains largely unexplored. Here, we generated the open access curatedFoodMetagenomicData (cFMD) resource by integrating 1,950 newly sequenced and 583 public food metagenomes. We produced 10,899 metagenome-assembled genomes spanning 1,036 prokaryotic and 108 eukaryotic species-level genome bins (SGBs), including 320 previously undescribed taxa. Food SGBs displayed significant microbial diversity within and between food categories. Extension to >20,000 human metagenomes revealed that food SGBs accounted on average for 3% of the adult gut microbiome. Strain-level analysis highlighted potential instances of food-to-gut transmission and intestinal colonization (e.g., Lacticaseibacillus paracasei) as well as SGBs with divergent genomic structures in food and humans (e.g., Streptococcus gallolyticus and Limosilactobabillus mucosae). The cFMD expands our knowledge on food microbiomes, their role in shaping the human microbiome, and supports future uses of metagenomics for food quality, safety, and authentication.},
}
@article {pmid39213166,
year = {2024},
author = {Djeghout, B and Le-Viet, T and Martins, LO and Savva, GM and Evans, R and Baker, D and Page, A and Elumogo, N and Wain, J and Janecko, N},
title = {Capturing clinically relevant Campylobacter attributes through direct whole genome sequencing of stool.},
journal = {Microbial genomics},
volume = {10},
number = {8},
pages = {},
doi = {10.1099/mgen.0.001284},
pmid = {39213166},
issn = {2057-5858},
mesh = {*Feces/microbiology ; Humans ; *Campylobacter/genetics/isolation &amp; purification/classification ; *Whole Genome Sequencing/methods ; *Campylobacter Infections/microbiology ; Genome, Bacterial ; Metagenome ; Metagenomics/methods ; Diarrhea/microbiology ; Phylogeny ; },
abstract = {Campylobacter is the leading bacterial cause of infectious intestinal disease, but the pathogen typically accounts for a very small proportion of the overall stool microbiome in each patient. Diagnosis is even more difficult due to the fastidious nature of Campylobacter in the laboratory setting. This has, in part, driven a change in recent years, from culture-based to rapid PCR-based diagnostic assays which have improved diagnostic detection, whilst creating a knowledge gap in our clinical and epidemiological understanding of Campylobacter genotypes - no isolates to sequence. In this study, direct metagenomic sequencing approaches were used to assess the possibility of replacing genome sequences with metagenome sequences; metagenomic sequencing outputs were used to describe clinically relevant attributes of Campylobacter genotypes. A total of 37 diarrhoeal stool samples with Campylobacter and five samples with an unknown pathogen result were collected and processed with and without filtration, DNA was extracted, and metagenomes were sequenced by short-read sequencing. Culture-based methods were used to validate Campylobacter metagenome-derived genome (MDG) results. Sequence output metrics were assessed for Campylobacter genome quality and accuracy of characterization. Of the 42 samples passing quality checks for analysis, identification of Campylobacter to the genus and species level was dependent on Campylobacter genome read count, coverage and genome completeness. A total of 65% (24/37) of samples were reliably identified to the genus level through Campylobacter MDG, 73% (27/37) by culture and 97% (36/37) by qPCR. The Campylobacter genomes with a genome completeness of over 60% (n=21) were all accurately identified at the species level (100%). Of those, 72% (15/21) were identified to sequence types (STs), and 95% (20/21) accurately identified antimicrobial resistance (AMR) gene determinants. Filtration of stool samples enhanced Campylobacter MDG recovery and genome quality metrics compared to the corresponding unfiltered samples, which improved the identification of STs and AMR profiles. The phylogenetic analysis in this study demonstrated the clustering of the metagenome-derived with culture-derived genomes and revealed the reliability of genomes from direct stool sequencing. Furthermore, Campylobacter genome spiking percentages ranging from 0 to 2% total metagenome abundance in the ONT MinION sequencer, configured to adaptive sequencing, exhibited better assembly quality and accurate identification of STs, particularly in the analysis of metagenomes containing 2 and 1% of Campylobacter jejuni genomes. Direct sequencing of Campylobacter from stool samples provides clinically relevant and epidemiologically important genomic information without the reliance on cultured genomes.},
}
@article {pmid39212408,
year = {2024},
author = {Child, HT and Airey, G and Maloney, DM and Parker, A and Wild, J and McGinley, S and Evens, N and Porter, J and Templeton, K and Paterson, S and van Aerle, R and Wade, MJ and Jeffries, AR and Bassano, I},
title = {Erratum for Child et al., "Comparison of metagenomic and targeted methods for sequencing human pathogenic viruses from wastewater".},
journal = {mBio},
volume = {},
number = {},
pages = {e0255824},
doi = {10.1128/mbio.02558-24},
pmid = {39212408},
issn = {2150-7511},
}
@article {pmid39212280,
year = {2024},
author = {Taylor, W and Devane, ML and Russell, K and Lin, S and Roxburgh, C and Williamson, J and Gilpin, BJ},
title = {Metagenomic evaluation of bacteria in drinking water using full-length 16S rRNA amplicons.},
journal = {Journal of water and health},
volume = {22},
number = {8},
pages = {1429-1443},
pmid = {39212280},
issn = {1477-8920},
support = {Strategic Science Internal Funding (SSIF)//Ministry of Business, Innovation and Employment/ ; },
mesh = {*Drinking Water/microbiology ; *RNA, Ribosomal, 16S/analysis/genetics ; *Metagenomics/methods ; *Water Microbiology ; *Bacteria/genetics/classification/isolation &amp; purification ; Water Purification ; Escherichia coli/isolation &amp; purification/genetics ; Feces/microbiology ; Environmental Monitoring/methods ; },
abstract = {Escherichia coli and total coliforms are important tools for identifying potential faecal contamination in drinking water. However, metagenomics offers a powerful approach for delving deeper into a bacterial community when E. coli or total coliforms are detected. Metagenomics can identify microbes native to water systems, track community changes and potential pathogens introduced by contamination events, and evaluate the effectiveness of treatment processes. Here, we demonstrate how the dual application of traditional monitoring practices and metagenomics can improve monitoring and surveillance for water resource management. The robustness of long-read metagenomics across replicates is demonstrated by the effect and interaction between manganese filters and bacterial communities, as well as the impact of chlorination after coliform detection. These examples reveal how metagenomics can identify the complex bacterial communities in the distribution system and the source waters used to supply drinking water treatment plants (DWTPs). The knowledge gained increases confidence in identified causes and mitigations of potential contamination events. By exploring bacterial communities, we can gain additional insights into the impact of faecal contamination events and treatment processes. This insight enables more precise remediation actions and enhances confidence in communicating health risks to drinking water operators and the public.},
}
@article {pmid39211470,
year = {2024},
author = {Graboski, AL and Simpson, JB and Pellock, SJ and Mehta, N and Creekmore, BC and Ariyarathna, Y and Bhatt, AP and Jariwala, PB and Sekela, JJ and Kowalewski, ME and Barker, NK and Mordant, AL and Borlandelli, VB and Overkleeft, H and Herring, LE and Jin, J and I James, L and Redinbo, MR},
title = {Advanced piperazine-containing inhibitors target microbial β-glucuronidases linked to gut toxicity.},
journal = {RSC chemical biology},
volume = {5},
number = {9},
pages = {853-865},
pmid = {39211470},
issn = {2633-0679},
support = {R01 GM135218/GM/NIGMS NIH HHS/United States ; R01 GM137286/GM/NIGMS NIH HHS/United States ; R35 GM152079/GM/NIGMS NIH HHS/United States ; },
abstract = {The gut microbiome plays critical roles in human homeostasis, disease progression, and pharmacological efficacy through diverse metabolic pathways. Gut bacterial β-glucuronidase (GUS) enzymes reverse host phase 2 metabolism, in turn releasing active hormones and drugs that can be reabsorbed into systemic circulation to affect homeostasis and promote toxic side effects. The FMN-binding and loop 1 gut microbial GUS proteins have been shown to drive drug and toxin reactivation. Here we report the structure-activity relationships of two selective piperazine-containing bacterial GUS inhibitors. We explore the potency and mechanism of action of novel compounds using purified GUS enzymes and co-crystal structures. Our results establish the importance of the piperazine nitrogen placement and nucleophilicity as well as the presence of a cyclohexyl moiety appended to the aromatic core. Using these insights, we synthesized an improved microbial GUS inhibitor, UNC10206581, that potently inhibits both the FMN-binding and loop 1 GUS enzymes in the human gut microbiome, does not inhibit bovine GUS, and is non-toxic within a relevant dosing range. Kinetic analyses demonstrate that UNC10206581 undergoes a slow-binding and substrate-dependent mechanism of inhibition similar to that of the parent scaffolds. Finally, we show that UNC10206581 displays potent activity within the physiologically relevant systems of microbial cultures and human fecal protein lysates examined by metagenomic and metaproteomic methods. Together, these results highlight the discovery of more effective bacterial GUS inhibitors for the alleviation of microbe-mediated homeostatic dysregulation and drug toxicities and potential therapeutic development.},
}
@article {pmid39211202,
year = {2024},
author = {Grodner, B and Wu, DT and Hahm, S and Takayasu, L and Wen, N and Kim, DM and Chen, CY and De Vlaminck, I},
title = {Microscale Spatial Dysbiosis in Oral biofilms Associated with Disease.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.07.24.604873},
pmid = {39211202},
issn = {2692-8205},
abstract = {Microbiome dysbiosis has largely been defined using compositional analysis of metagenomic sequencing data; however, differences in the spatial arrangement of bacteria between healthy and diseased microbiomes remain largely unexplored. In this study, we measured the spatial arrangement of bacteria in dental implant biofilms from patients with healthy implants, peri-implant mucositis, or peri-implantitis, an oral microbiome-associated inflammatory disease. We discovered that peri-implant biofilms from patients with mild forms of the disease were characterized by large single-genus patches of bacteria, while biofilms from healthy sites were more complex, mixed structures. Based on these findings, we propose a model of peri-implant dysbiosis where changes in biofilm spatial architecture allow the colonization of new community members. This model indicates that spatial structure could be used as a potential biomarker for community stability and has implications in diagnosis and treatment of peri-implant diseases. These results enhance our understanding of peri-implant disease pathogenesis and may be broadly relevant for spatially structured microbiomes.},
}
@article {pmid39210977,
year = {2024},
author = {Ekpruke, CD and Alford, R and Rousselle, D and Babayev, M and Sharma, S and Parker, E and Davis, K and Hemmerich, C and Rusch, DB and Silveyra, P},
title = {Sex-specific alterations in the gut and lung microbiome of allergen-induced mice.},
journal = {Frontiers in allergy},
volume = {5},
number = {},
pages = {1451846},
pmid = {39210977},
issn = {2673-6101},
abstract = {INTRODUCTION: Recent evidence has demonstrated that the microbiome is a driver of the underlying pathophysiological mechanisms of respiratory disease. Studies have indicated that bacterial metabolites produced in the gut and lung can impact lung inflammation and immune cell activity, affecting disease pathology. Despite asthma being a disease with marked sex differences, experimental work linking microbiomes and asthma has not considered the sex variable.<br><br>METHODS: To test the hypothesis that the lung and gut microbial composition impacts allergic lung inflammation in a sex-specific manner, we evaluated lung and gut microbiome alterations in a mouse model of allergic inflammation and assessed their association with lung function and inflammation phenotypes. For this, we exposed male and female adult C57BL/6J mice intranasally to 25&#x2005;&#xb5;g of a house dust mite extract mix (HDM) daily, or phosphate-buffered saline (PBS) as control, for 5 weeks (n&#x2009;=&#x2009;4-6/group). DNA from fecal pellets collected before and after the 5-week treatment, and from lung tissue collected at endpoint, was extracted using the ZymoBIOMICS&#xae;-96 MagBead DNA Kit and analyzed to determine the 16S microbiome via Targeted Metagenomic Sequencing.<br><br>RESULTS: The HDM treatment induced a sex-specific allergic inflammation phenotype with significantly higher neutrophilia, lymphocytosis, inflammatory gene expression, and histopathological changes in females than males following exposure to HDM, but higher airway hyperresponsiveness (AHR) in males than females. In addition, sex-specific lung gene expression and associated pathways were identified HDM mix after challenge. These changes corresponded to sex-specific alterations in the gut microbiome, where the Firmicutes to Bacteroidetes ratio (F:B) was significantly reduced in fecal samples from only male mice after HDM challenge, and alpha diversity was increased in males, but decreased in females, after 5-weeks of HDM treatment.<br><br>DISCUSSION: Overall, our findings indicate that intranasal allergen challenge triggers sex-specific changes in both gut and lung microbiomes, and induces sex-specific lung inflammation, AHR, and lung inflammatory gene expression pathways, suggesting a contribution of the lung-gut axis in allergic airway disease.},
}
@article {pmid39210818,
year = {2024},
author = {Souza, KL and Dias, CP and Callegari, MA and Friderichs, A and Paes, AOS and Carvalho, RH and Silva, CA},
title = {Performance and intestinal health of piglets in the nursery phase subjected to diets with condensed black wattle (Acacia mearnsii) tannin.},
journal = {Animal bioscience},
volume = {},
number = {},
pages = {},
doi = {10.5713/ab.24.0112},
pmid = {39210818},
issn = {2765-0189},
abstract = {OBJECTIVE: The objective of this study was to evaluate the use of condensed tannin from black acacia (Acacia mearnsii) as a substitute additive for zinc oxide and growth-promoting antibiotics on the performance, digestibility, and intestinal health of piglets in the nursery phase.<br><br>METHODS: A total of 200 PIC&#xae; piglets that were 22 days old and weighed 6.0&#xb1;0.9 kg were subjected to four treatments in the nursery phase (22 to 64 days of age): CONTR (control diet); ENR+ZnO (control diet + 10 mg/kg of enramycin + 2,500 mg/kg of zinc oxide during the first 21 days); BUT (control diet + 900 mg/kg of sodium butyrate) and TAN (control diet + 2,000 mg/kg of condensed tannin). The experimental design was a randomized block with 4 treatments and 10 replicates, with a pen of five animals each as the experimental unit. The zootechnical performance, diarrhea index score, dietary digestibility and metagenomics of the deep rectum microbiota were evaluated.<br><br>RESULTS: The TAN had greater weight gain in the nursery phase and final weight (p<0.05) than the CONTR (394 vs. 360 g/d, and 22.6 vs. 21.1 kg, respectively), with these values being intermediate for the ENR+ZnO and BUT (365 and 382 g/d, and 21.3 and 22.1 kg, respectively). There was no difference between treatments for semi-liquid diarrhea (score 2), but CONTR had more cases of severe diarrhea (score 3; p<0.05) than ENR+ZnO, BUT and TAN, with 42, 18, 29 and 21 cases, respectively. The treatments had no impact on rare taxa or the relative abundances of taxonomic groups (uniformity), but the use of TAN promoted an increase in the abundances of Brevibacillus spp. and Enterococcus spp. compared to the other treatments (p<0.05).<br><br>CONCLUSION: The use of condensed tannin from black wattle as a performance-enhancing additive was effective, with effects on performance and intestinal health, demonstrating its potential as a substitute for zinc oxide and enramycin in the diets of piglets in nursery phase.},
}
@article {pmid39210613,
year = {2024},
author = {Xu, Y and Wu, X and Li, Y and Liu, X and Fang, L and Jiang, Z},
title = {Probiotics and the Role of Dietary Substrates in Maintaining the Gut Health: Use of Live Microbes and Their Products for Anticancer Effects against Colorectal Cancer.},
journal = {Journal of microbiology and biotechnology},
volume = {34},
number = {9},
pages = {1-14},
doi = {10.4014/jmb.2403.03056},
pmid = {39210613},
issn = {1738-8872},
abstract = {The gut microbiome is an important and the largest endocrine organ linked to the microbes of the GI tract. The bacterial, viral and fungal communities are key regulators of the health and disease status in a host at hormonal, neurological, immunological, and metabolic levels. The useful microbes can compete with microbes exhibiting pathogenic behavior by maintaining resistance against their colonization, thereby maintaining eubiosis. As diagnostic tools, metagenomic, proteomic and genomic approaches can determine various microbial markers in clinic for early diagnosis of colorectal cancer (CRC). Probiotics are live non-pathogenic microorganisms such as lactic acid bacteria, Bifidobacteria, Firmicutes and Saccharomyces that can help maintain eubiosis when administered in appropriate amounts. In addition, the type of dietary intake contributes substantially to the composition of gut microbiome. The use of probiotics has been found to exert antitumor effects at preclinical levels and promote the antitumor effects of immunotherapeutic drugs at clinical levels. Also, modifying the composition of gut microbiota by Fecal Microbiota Transplantation (FMT), and using live lactic acid producing bacteria such as Lactobacillus, Bifidobacteria and their metabolites (termed postbiotics) can contribute to immunomodulation of the tumor microenvironment. This can lead to tumor-preventive effects at early stages and antitumor effects after diagnosis of CRC. To conclude, probiotics are presumably found to be safe to use in humans and are to be studied further to promote their appliance at clinical levels for management of CRC.},
}
@article {pmid39210307,
year = {2024},
author = {Zheng, Y and Liu, W and Xiao, T and Chen, H and Liu, Y},
title = {Clinical utility of metagenomic next-generation sequencing on bronchoalveolar lavage fluid in diagnosis of lower respiratory tract infections.},
journal = {BMC pulmonary medicine},
volume = {24},
number = {1},
pages = {422},
pmid = {39210307},
issn = {1471-2466},
support = {2019A1515110566//Basic and Applied Basic Research Foundation of Guangdong Province/ ; },
mesh = {Humans ; *Bronchoalveolar Lavage Fluid/microbiology ; *High-Throughput Nucleotide Sequencing/methods ; Male ; Retrospective Studies ; Female ; Middle Aged ; *Respiratory Tract Infections/diagnosis/microbiology ; *Metagenomics/methods ; Adult ; Aged ; Sensitivity and Specificity ; Young Adult ; },
abstract = {BACKGROUND: In this study, we aimed to evaluate the clinical utility of Metagenomic Next-Generation sequencing (mNGS) on bronchoalveolar lavage fluid (BALF) in diagnosis of Lower Respiratory Tract Infections (LRTIs).<br><br>METHODS: In this study, we retrospectively analyzed 186 hospitalized patients who were suspected with LRTIs and performed mNGS (DNA) test of BALF simultaneously at The Fifth Affiliated Hospital of Sun Yat-Sen University from March 2023 to August 2023. Suspected LRTI was based on LRTI related clinical manifestations or imaging examination. Among them, 155 patients had undergone conventional culture and mNGS (DNA) testing simultaneously. Finally, 138 cases (89.03%,138/155) were diagnosed as LRTI and 17 cases (10.97%,17/155) were diagnosed as non-LRTI. Both detecting rate and diagnostic efficacy of mNGS and conventional culture were compared.<br><br>RESULTS: The positive detection rates of pathogens between mNGS and conventional culture were significant different (81.29% VS 39.35%, P&#x2009;<&#x2009;0.05). Compared with paired conventional culture result, the sensitivity of mNGS in diagnosis of LRTIs was more superior (88.41% VS 43.48%; P&#x2009;<&#x2009;0.05), the specificity was opposite (76.47% VS 94.12%; P&#x2009;>&#x2009;0.05). Furthermore, 77.54% and 35.51% of LRTI cases were being etiologically diagnosed by mNGS and culture respectively. Importantly, mNGS directly led to a change of treatment regimen in 58 (37.42%) cases, including antibiotic adjustment (29.68%) and ruling out active infection (7.74%). Moreover, treatment regimen remained unchanged in 97 (62.58%) cases, considering the current antibiotic therapy already covered the detected pathogens (36.13%) or empirical treatment was effective (11.61%).<br><br>CONCLUSIONS: mNGS can identify a wide range of pathogens in LRTIs, with improved sensitivity and being more superior at diagnosing LRTIs etiologically. mNGS has the potential to enhance clinical outcomes by optimizing the treatment regimens.},
}
@article {pmid39210095,
year = {2024},
author = {Lu, J and Rincon, N and Wood, DE and Breitwieser, FP and Pockrandt, C and Langmead, B and Salzberg, SL and Steinegger, M},
title = {Author Correction: Metagenome analysis using the Kraken software suite.},
journal = {Nature protocols},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41596-024-01064-1},
pmid = {39210095},
issn = {1750-2799},
}
@article {pmid39209985,
year = {2024},
author = {Maini Rekdal, V and Villalobos-Escobedo, JM and Rodriguez-Valeron, N and Olaizola Garcia, M and Prado Vásquez, D and Rosales, A and Sörensen, PM and Baidoo, EEK and Calheiros de Carvalho, A and Riley, R and Lipzen, A and He, G and Yan, M and Haridas, S and Daum, C and Yoshinaga, Y and Ng, V and Grigoriev, IV and Munk, R and Wijaya, CH and Nuraida, L and Damayanti, I and Cruz-Morales, P and Keasling, JD},
title = {Neurospora intermedia from a traditional fermented food enables waste-to-food conversion.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {39209985},
issn = {2058-5276},
abstract = {Fungal fermentation of food and agricultural by-products holds promise for improving food sustainability and security. However, the molecular basis of fungal waste-to-food upcycling remains poorly understood. Here we use a multi-omics approach to characterize oncom, a fermented food traditionally produced from soymilk by-products in Java, Indonesia. Metagenomic sequencing of samples from small-scale producers in Western Java indicated that the fungus Neurospora intermedia dominates oncom. Further transcriptomic, metabolomic and phylogenomic analysis revealed that oncom-derived N. intermedia utilizes pectin and cellulose degradation during fermentation and belongs to a genetically distinct subpopulation associated with human-generated by-products. Finally, we found that N. intermedia grew on diverse by-products such as fruit and vegetable pomace and plant-based milk waste, did not encode mycotoxins, and could create foods that were positively perceived by consumers outside Indonesia. These results showcase the traditional significance and future potential of fungal fermentation for creating delicious and nutritious foods from readily available by-products.},
}
@article {pmid39209935,
year = {2024},
author = {Starkova, D and Gladyshev, N and Polev, D and Saitova, A and Egorova, S and Svarval, A},
title = {First insight into the whole genome sequence variations in clarithromycin resistant Helicobacter pylori clinical isolates in Russia.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {20108},
pmid = {39209935},
issn = {2045-2322},
mesh = {*Clarithromycin/pharmacology ; *Helicobacter pylori/genetics/drug effects ; Russia/epidemiology ; Humans ; *Drug Resistance, Bacterial/genetics ; *Anti-Bacterial Agents/pharmacology ; *Microbial Sensitivity Tests ; *Whole Genome Sequencing/methods ; *Helicobacter Infections/microbiology/drug therapy ; Mutation ; RNA, Ribosomal, 23S/genetics ; Genome, Bacterial ; Male ; Genetic Variation ; Female ; Adult ; Middle Aged ; Aged ; },
abstract = {Clarithromycin (CLR) is currently a key antibiotic for Helicobacter pylori infection treatment, however, the data on CLR resistance patterns in Russia are missing. Here, we applied WGS-based approach to H. pylori clinical isolates from Russia to comprehensively investigate sequence variation, identify putative markers of CLR resistance and correlate them with phenotypic susceptibility testing. The phenotypic susceptibility of 44 H. pylori isolates (2014-2022) to CLR was determined by disc diffusion method: 23 isolates were CLR-resistant and 21-CLR-susceptible. All isolates were subjected to WGS and submitted to GenBank. Based on complete sequence analysis, we showed that among all sequence variants, the combination of mutations A2146G/A2147G in the 23S rRNA gene is the most reliable for prediction of phenotypic susceptibility. For the first time, the average number of mutations in 106 virulence-associated genes between resistant and susceptible groups were compared. Moreover, this study presents the first WGS insight into genetic diversity of H. pylori in Russia with a particular focus on the molecular basis of drug resistance: the novel mutations were described as potential markers for the resistance development. Of these, the most prominent was a frameshift deletion (252:CGGGT) in HP0820 coding region, which is a good candidate for further investigation.},
}
@article {pmid39209855,
year = {2024},
author = {Whittle, MJ and Castillo-Fernandez, J and Amos, GCA and Watson, P},
title = {Metagenomic characterisation of canine skin reveals a core healthy skin microbiome.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {20104},
pmid = {39209855},
issn = {2045-2322},
mesh = {Dogs ; Animals ; *Skin/microbiology ; *Microbiota ; *Metagenomics/methods ; Metagenome ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; },
abstract = {Furthering our knowledge of the skin microbiome is essential to understand health and disease in canines. To date, studies into the canine skin microbiome have focused on 16S rRNA high throughput sequencing however, these lack the granularity of species and strain level taxonomic characterisation and their associated functions. The aim of this study was to provide a comprehensive assessment of the skin microbiome by analysing the skin microbiome of 72 healthy adult colony dogs, across four distinct skin sites and four breeds, using metagenomic sequencing. Our analysis revealed that breed and skin site are drivers of variation, and a core group of taxa and genes are present within the skin microbiome of healthy dogs, comprising 230 taxa and 1219 gene families. We identified 15 species within the core microbiome that are represented by more than one strain. The biosynthesis of secondary metabolites pathway was enriched in the core microbiome suggesting the skin microbiome may play a role in colonisation resistance and protection from invading pathogens. Additionally, we uncovered the novelty of the canine skin microbiome and show that further investigation is required to increase the suitability of current databases for metagenomic sequencing of canine skin samples.},
}
@article {pmid39209553,
year = {2024},
author = {Sapci, AOB and Mirarab, S},
title = {Memory-bound k-mer selection for large and evolutionary diverse reference libraries.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.279339.124},
pmid = {39209553},
issn = {1549-5469},
abstract = {Using k-mers to find sequence matches is increasingly used in many bioinformatic applications, including metagenomic sequence classification. The accuracy of these downstream applications relies on the density of the reference databases, which are rapidly growing. While the increased density provides hope for dramatic improvements in accuracy, scalability is a concern. The k-mers are kept in the memory during the query time, and saving all k-mers of these ever-expanding databases is fast becoming impractical. Several strategies for subsampling k-mers have been proposed, including minimizers and finding taxon-specific k-mers. However, we contend that these strategies are inadequate, especially when reference sets are taxonomically imbalanced, as are most microbial libraries. In this paper, we explore approaches for selecting a fixed-size subset of k-mers present in an ultra-large dataset to include in a library such that the classification of reads suffers the least. Our experiments demonstrate the limitations of existing approaches, especially for novel and poorly sampled groups. We propose a library construction algorithm called KRANK (K-mer RANKer) that combines several components, including a hierarchical selection strategy with adaptive size restrictions and an equitable coverage strategy. We implement KRANK in highly optimized code and combine it with the locality-sensitive-hashing classifier CONSULT-II to build a taxonomic classification and profiling method. On several benchmarks, KRANK k-mer selection dramatically reduces memory consumption with minimal loss in classification accuracy. We show in extensive analyses based on CAMI benchmarks that KRANK outperforms k-mer-based alternatives in terms of taxonomic profiling and comes close to the best marker-based methods in terms of accuracy.},
}
@article {pmid39209175,
year = {2024},
author = {Dong, Q and Sun, B and Liu, Y and Huang, X},
title = {Sewerage surveillance tracking characteristics of human antibiotic resistance genes in sewer system.},
journal = {The Science of the total environment},
volume = {952},
number = {},
pages = {175850},
doi = {10.1016/j.scitotenv.2024.175850},
pmid = {39209175},
issn = {1879-1026},
mesh = {*Sewage/microbiology ; Humans ; *Drug Resistance, Microbial/genetics ; *Environmental Monitoring/methods ; Anti-Bacterial Agents/analysis ; COVID-19 ; Wastewater/microbiology ; Drug Resistance, Bacterial/genetics ; Waste Disposal, Fluid ; Genes, Bacterial ; },
abstract = {Sewage surveillance is widely applied to track valid human excretion information and identify public health conditions during corona virus disease 2019 (COVID-19) pandemic. This approach can be applied to monitor the antibiotic resistance level in sewers and to assess the risk of spreading antibiotic resistance in municipal wastewater systems. However, there is still little information about human antibiotic resistance occurrence characteristics in sewer system. This study conducted a field trial for whole year to advance understanding on spatial and temporal occurrence of antibiotic resistance genes (ARGs) in gravity sewerage. The spatial distribution of ARGs along the drainage pipe line (from human settlements to wastewater treatement pant (WWTP)) was insignificant, which may be affected by irregular human emission alongside the pipeline. The correlation between ARGs and antibiotics in sewage was insignificant. The temporal distribution showed that the effect of temperature on ARGs abundance was evident, the ARGs abundance in sewage was generally higher during the cold season. Metagenomic analysis revealed that the detected ARGs were mainly distributed in Proteobacteria (47.51 %) and Antinobacteria (20.11 %). Potential hosts of ARGs in sewage were mainly identified as human gut microorganisms, including human pathogenic bacteria, such as Prevotella, Kocuria, and Propionibacterium, etc. This study provides a new insight into the sewerage surveillance tracking characteristics of human ARGs in sewer system, and suggesting that the sewage-carried ARGs surveillance is a promising method for assessment and management of antibiotic resistance level on population size.},
}
@article {pmid39208976,
year = {2024},
author = {Su, Z and Cui, S and Wen, D and Chen, L},
title = {Metagenomic insights into resistome, mobilome and virulome in different fecal waste.},
journal = {Environmental research},
volume = {262},
number = {Pt 1},
pages = {119861},
doi = {10.1016/j.envres.2024.119861},
pmid = {39208976},
issn = {1096-0953},
abstract = {Fecal waste is a significant source of antimicrobial resistance (AMR) pollution and provides valuable insights into the AMR development in animal and human populations within the "One health" framework. Various genetic elements, including antibiotic resistance genes (ARGs), biocide and metal resistance genes (BMGs), mobile genetic elements (MGEs), and virulence factor genes (VFGs), are crucial AMR risk determinants (ARDs). However, few studies focused on compositional characteristics of ARDs in different feces. Here, we analyzed 753 public metagenomes from human, pig, chicken, and cattle feces, revealing significant differences in ARD richness and abundance across fecal types, notably lowest in cattle samples. Tetracycline, multi-metal, and -biocide resistance genes were dominant resistome. A few core genes contributed to 25.6%-91.1% of gene abundance, and their correlations were stronger in cattle samples. Procrustes analysis showed that microbial composition had higher correlations with ARGs (M[2] = 0.579) and BMGs (M[2] = 0.519). Gammaproteobacteria was identified as major ARD-hosts especially in human and pig feces, and they mainly carried multi-resistance genes. MGEs exhibited direct positive effects on ARGs and BMGs, indirectly impacting VFGs. Utilizing random forest methods, we identified 42 indicator genes for tracking AMR pollution originating from fecal sources in the environments. This study offers new insights into understanding and controlling the AMR pollution of fecal waste from human and food animals.},
}
@article {pmid39208627,
year = {2024},
author = {Chen, T and Deng, C and Li, S and Li, B and Liang, Y and Zhang, Y and Li, J and Xu, N and Yu, K},
title = {Multi-omics illuminates the functional significance of previously unknown species in a full-scale landfill leachate treatment plant.},
journal = {Journal of hazardous materials},
volume = {479},
number = {},
pages = {135669},
doi = {10.1016/j.jhazmat.2024.135669},
pmid = {39208627},
issn = {1873-3336},
mesh = {*Water Pollutants, Chemical/metabolism/analysis ; *Bacteria/genetics/metabolism ; *Biodegradation, Environmental ; Archaea/genetics/metabolism ; Waste Disposal Facilities ; Metagenomics ; Multiomics ; },
abstract = {Landfill leachate treatment plants (LLTPs) harbor a vast reservoir of uncultured microbes, yet limited studies have systematically unraveled their functional potentials within LLTPs. Combining 36 metagenomic and 18 metatranscriptomic datasets from a full-scale LLTP, we unveiled a double-edged sword role of unknown species in leachate biotreatment and environmental implication. We identified 655 species-level genome bins (SGBs) spanning 47 bacterial and 3 archaeal phyla, with 75.9 % unassigned to any known species. Over 90 % of up-regulated functional genes in biotreatment units, compared to the leachate influent, were carried by unknown species and actively participated in carbon, nitrogen, and sulfur cycles. Approximately 79 % of the 37,366 carbohydrate active enzymes (CAZymes), with ∼90 % novelty and high expression, were encoded by unknown species, exhibiting great potential in biodegrading carbohydrate compounds linked to human meat-rich diets. Unknown species offered a valuable genetic resource of thousands of versatile, abundant, and actively expressed metabolic gene clusters (MGCs) and biosynthetic gene clusters (BGCs) for enhancing leachate treatment. However, unknown species may contribute to the emission of hazardous N2O/H2S and represented significant reservoirs for antibiotic-resistant pathogens that posed environmental safety risks. This study highlighted the significance of considering both positive and adverse effects of LLTP microbes to optimize LLTP performance.},
}
@article {pmid39207726,
year = {2024},
author = {Lu, C and Wang, X and Ye, P and Lu, Z and Ma, J and Luo, W and Wang, S and Chen, X},
title = {Antimicrobial peptides from the gut microbiome of the centenarians: diversification of biosynthesis and youthful development of resistance genes.},
journal = {The journals of gerontology. Series A, Biological sciences and medical sciences},
volume = {},
number = {},
pages = {},
doi = {10.1093/gerona/glae218},
pmid = {39207726},
issn = {1758-535X},
abstract = {Antimicrobial peptides (AMPs) offer a potential solution to the antibiotic crisis owing to their antimicrobial properties, and the human gut biome may be a source of these peptides. However, the potential AMPs and antimicrobial peptide resistance genes (AMPRGs) of gut microbes in different age groups has not been thoroughly assessed. Here, we investigated the potential development of AMPs and the distribution pattern of AMPRGs in the gut microbiome at different ages by analyzing the intestinal metagenomic data of healthy individuals at different life stages (CG: centenarians group n=20; OAG: older adults group n=15; YG: young group n=15). Age-related increases were observed in the potential AMPs within the gut microbiome, with centenarians showing a greater diversity of these peptides. However, the gut microbiome of the CG group had a lower level of AMPRGs compared to that of the OAG group, and it was similar to the level found in the YG group. Additionally, conventional probiotic strains showed a significant positive correlation with certain potential AMPs and were associated with a lower detection of resistance genes. Additionally, comparing potential AMPs with existing libraries revealed limited similarity, indicating that current machine-learning models can identify novel peptides in the gut microbiota. These results indicate that longevity may benefit from diversity of AMPs and lower resistance genes. Our findings help explain the age advantage of the centenarians and identify the potential for antimicrobial peptide biosynthesis in the human gut microbiome, offering insights into the development of antimicrobial peptide resistance and the screening of probiotic strains.},
}
@article {pmid39207532,
year = {2024},
author = {Laczi, K and Bodor, A and Kovács, T and Magyar, B and Perei, K and Rákhely, G},
title = {Methanogenesis coupled hydrocarbon biodegradation enhanced by ferric and sulphate ions.},
journal = {Applied microbiology and biotechnology},
volume = {108},
number = {1},
pages = {449},
pmid = {39207532},
issn = {1432-0614},
support = {EFOP-3.6.2-16-2017-00010//The European Union and the State of Hungary/ ; NTP-NFT&#xd6;-20-B-0027//Hungarian Prime Minister's Office/ ; 7036//University of Szeged Open Access Found/ ; },
mesh = {*Biodegradation, Environmental ; *Sulfates/metabolism ; *Methane/metabolism ; *Hydrocarbons/metabolism ; *Soil Microbiology ; Bacteria/metabolism/genetics/classification ; Ferric Compounds/metabolism ; Metagenome ; Soil Pollutants/metabolism ; },
abstract = {Bioremediation provides an environmentally sound solution for hydrocarbon removal. Although bioremediation under anoxic conditions is slow, it can be coupled with methanogenesis and is suitable for energy recovery. By altering conditions and supplementing alternative terminal electron acceptors to the system to induce syntrophic partners of the methanogens, this process can be enhanced. In this study, we investigated a hydrocarbon-degrading microbial community derived from chronically contaminated soil. Various hydrocarbon mixtures were used during our experiments in the presence of different electron acceptors. In addition, we performed whole metagenome sequencing to identify the main actors of hydrocarbon biodegradation in the samples. Our results showed that the addition of ferric ions or sulphate increased the methane yield. Furthermore, the addition of CO2, ferric ion or sulphate enhanced the biodegradation of alkanes. A significant increase in biodegradation was observed in the presence of ferric ions or sulphate in the case of all aromatic components, while naphthalene and phenanthrene degradation was also enhanced by CO2. Metagenome analysis revealed that Cellulomonas sp. is the most abundant in the presence of alkanes, while Ruminococcus and Faecalibacterium spp. are prevalent in aromatics-supplemented samples. From the recovery of 25 genomes, it was concluded that the main pathway of hydrocarbon activation was fumarate addition in both Cellulomonas, Ruminococcus and Faecalibacterium. Chloroflexota bacteria can utilise the central metabolites of aromatics biodegradation via ATP-independent benzoyl-CoA reduction. KEY POINTS: • Methanogenesis and hydrocarbon biodegradation were enhanced by Fe[3+] or SO4[2-] • Cellulomonas, Ruminococcus and Faecalibacterium can be candidates for the main hydrocarbon degraders • Chloroflexota bacteria can utilise the central metabolites of aromatics degradation.},
}
@article {pmid39207169,
year = {2024},
author = {Baker, BJ and Sarno, N},
title = {Small archaea may form intimate partnerships to maximize their metabolic potential.},
journal = {mBio},
volume = {},
number = {},
pages = {e0034724},
doi = {10.1128/mbio.00347-24},
pmid = {39207169},
issn = {2150-7511},
abstract = {DPANN archaea have characteristically small cells and unique genomes that were long overlooked in diversity surveys. Their reduced genomes often lack essential metabolic pathways, requiring symbiotic relationships with other archaeal and bacterial hosts for survival. Yet a long-standing question remains, what is the advantage of maintaining ultrasmall cells. A recent study by Zhang et al. examined genomes of DPANN archaea from marine oxygen deficient zones (ODZs) (I. H. Zhang, B. Borer, R. Zhao, S. Wilbert, et al., mBio 15:e02918-23, 2024, https://doi.org/10.1128/mbio.02918-23). Surprisingly, these genomes contain a broad array of metabolic pathways including genes predicted to be involved in nitrous oxide (N2O) reduction. However, N2O levels are likely too low in ODZs to make this metabolically feasible. Modeling co-localization of DPANN archaea (N2O consumers) with other larger cells (N2O producers) demonstrates that N2O uptake rates can be optimized by maximizing the producer-to-consumer size ratio and proximity of consumer cells to producers. This may explain why such a diversity of archaea maintain extremely small cell sizes.},
}
@article {pmid39207108,
year = {2024},
author = {Crouch, AL and Monsey, L and Rambeau, M and Ramos, C and Yracheta, JM and Anderson, MZ},
title = {Metagenomic discovery of microbial eukaryotes in stool microbiomes.},
journal = {mBio},
volume = {},
number = {},
pages = {e0206324},
doi = {10.1128/mbio.02063-24},
pmid = {39207108},
issn = {2150-7511},
abstract = {Host-associated microbiota form complex microbial communities that are increasingly associated with host behavior and disease. While these microbes include bacterial, archaeal, viral, and eukaryotic constituents, most studies have focused on bacteria due to their dominance in the human host and available tools for investigation. Accumulating evidence suggests microbial eukaryotes in the microbiome play pivotal roles in host health, but our understandings of these interactions are limited to a few readily identifiable taxa because of technical limitations in unbiased eukaryote exploration. Here, we combined cell sorting, optimized eukaryotic cell lysis, and shotgun sequencing to accelerate metagenomic discovery and analysis of host-associated microbial eukaryotes. Using synthetic communities with a 1% microbial eukaryote representation, the eukaryote-optimized cell lysis and DNA recovery method alone yielded a 38-fold increase in eukaryotic DNA. Automated sorting of eukaryotic cells from stool samples of healthy adults increased the number of microbial eukaryote reads in metagenomic pools by up to 28-fold compared to commercial kits. Read frequencies for identified fungi increased by 10,000× on average compared to the Human Microbiome Project and allowed for the identification of novel taxa, de novo assembly of contigs from previously unknown microbial eukaryotes, and gene prediction from recovered genomic segments. These advances pave the way for the unbiased inclusion of microbial eukaryotes in deciphering determinants of health and disease in the host-associated microbiome.IMPORTANCEMicrobial eukaryotes are common constituents of the human gut where they can contribute to local ecology and host health, but they are often overlooked in microbiome studies. The lack of attention is due to current technical limitations that are heavily biased or poorly recovered DNA from microbial eukaryotes. We developed a method to increase the representation of these eukaryotes in metagenomic sequencing of microbiome samples that allows to improve their detection compared to prior methods and allows for the identification of new species. Application of the technique to gut microbiome samples improved detection of fungi, protists, and helminths. New eukaryotic taxa and their encoded genes could be identified by sequencing a small number of samples. This approach can improve the inclusion of eukaryotes into microbiome research.},
}
@article {pmid39206688,
year = {2024},
author = {Klier, KM and Martin, C and Langwig, MV and Anantharaman, K},
title = {Evolutionary history and origins of Dsr-mediated sulfur oxidation.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {39206688},
issn = {1751-7370},
support = {//UW-Madison Science and Medicine Graduate Research Fellowship (SciMed GRS)/ ; OCE2049478//National Science Foundation Graduate Research Fellowship/ ; //National Science Foundation/ ; },
mesh = {*Oxidation-Reduction ; *Sulfur/metabolism ; *Archaea/genetics/metabolism ; *Phylogeny ; *Bacteria/genetics/metabolism/classification ; Evolution, Molecular ; Hydrogensulfite Reductase/genetics/metabolism ; },
abstract = {Microorganisms play vital roles in sulfur cycling through the oxidation of elemental sulfur and reduction of sulfite. These metabolisms are catalyzed by dissimilatory sulfite reductases (Dsr) functioning in either the reductive or reverse, oxidative direction. Dsr-mediated sulfite reduction is an ancient metabolism proposed to have fueled energy metabolism in some of Earth's earliest microorganisms, whereas sulfur oxidation is believed to have evolved later in association with the widespread availability of oxygen on Earth. Organisms are generally believed to carry out either the reductive or oxidative pathway, yet organisms from diverse phyla have been discovered with gene combinations that implicate them in both pathways. A comprehensive investigation into the metabolisms of these phyla regarding Dsr is currently lacking. Here, we selected one of these phyla, the metabolically versatile candidate phylum SAR324, to study the ecology and evolution of Dsr-mediated metabolism. We confirmed that diverse SAR324 encode genes associated with reductive Dsr, oxidative Dsr, or both. Comparative analyses with other Dsr-encoding bacterial and archaeal phyla revealed that organisms encoding both reductive and oxidative Dsr proteins are constrained to a few phyla. Further, DsrAB sequences from genomes belonging to these phyla are phylogenetically positioned at the interface between well-defined oxidative and reductive bacterial clades. The phylogenetic context and dsr gene content in these organisms points to an evolutionary transition event that ultimately gave way to oxidative Dsr-mediated metabolism. Together, this research suggests that SAR324 and other phyla with mixed dsr gene content are associated with the evolution and origins of Dsr-mediated sulfur oxidation.},
}
@article {pmid39206173,
year = {2024},
author = {Yu, F and Zhang, X and Li, Y and Gai, W and Zheng, Y and Cai, X},
title = {Severe pneumonia with empyema due to multiple anaerobic infections: case report and literature review.},
journal = {Frontiers in medicine},
volume = {11},
number = {},
pages = {1435823},
pmid = {39206173},
issn = {2296-858X},
abstract = {BACKGROUND: Cases of severe pneumonia complicated by empyema due to normal anaerobic flora from the oral cavity are infrequent. Diagnosing anaerobic infections through conventional microbiological test (CMT) is often challenging.<br><br>CASE PRESENTATION: This study describes the case of a 67-year-old man, bedridden long-term, who developed severe pneumonia with empyema caused by multiple anaerobic bacterial infections. The patient was hospitalized with a 5-day history of cough, sputum and fever, accompanied by a 2-day history of dyspnea. Despite CMT, the specific etiology remained elusive. However, metagenomic next-generation sequencing (mNGS) identified various anaerobic bacteria in bronchoalveolar lavage fluid (BALF), blood and pleural effusion. The patient was diagnosed with a polymicrobial infection involving multiple anaerobic bacteria. Following treatment with metronidazole and moxifloxacin, the patient's pulmonary symptoms improved.<br><br>CONCLUSION: mNGS serves as a valuable adjunctive tool for diagnosting and managing patients whose etiology remains unidentified following CMT.},
}
@article {pmid39206169,
year = {2024},
author = {Zhou, Y and Zhai, Y and Wang, Y and Zhang, D and Feng, G},
title = {Case report: The use of metagenomic next-generation sequencing to diagnose Lemierre's syndrome caused by lost root canal fillings in a 33-year-old patient with metabolic syndrome.},
journal = {Frontiers in medicine},
volume = {11},
number = {},
pages = {1402444},
pmid = {39206169},
issn = {2296-858X},
abstract = {BACKGROUND: Lemierre's syndrome is a rare and serious complication of pharyngitis with an estimated annual incidence of 1 in 100,000 people worldwide. It is characterized by septic thrombophlebitis of the internal jugular vein with metastatic infection, usually after oropharyngeal infection. Rare cases of Lemierre's syndrome have been reported to be caused by odontogenic infection.<br><br>CASE REPORT: A 33-year-old male visited our hospital with symptoms of fever and sore throat for 16&#x2009;days. The other symptoms included pain in his left neck and shoulder. In addition, metabolic syndrome was diagnosed based on waist circumference, diabetes, and hyperlipidemia. Fusobacterium necrophorum bacteria was detected using the metagenomic next-generation sequencing (mNGS) technique. The enhanced computerized tomography (CT) scan showed thrombosis of the left proximal jugular vein and brachiocephalic vein. Based on these observations, Lemierre's syndrome was diagnosed. The etiology was that the fillings in the root canal tooth were lost with no blood or pain about 2&#x2009;weeks before the onset. The patient recovered after treatment with antibiotics and blood purification.<br><br>CONCLUSION: Lemierre's syndrome should be evaluated for patients with fever, sore throat, and neck pain. If the loss of fillings from root canal therapy occurs, especially for those with metabolic syndrome, we should be aware of the possibility of this disease. Furthermore, the mNGS test can be used as a crucial supplementary diagnostic tool for patients with undetermined fever.},
}
@article {pmid39206042,
year = {2024},
author = {Zhen, J and Zhang, Y and Li, Y and Zhou, Y and Cai, Y and Huang, G and Xu, A},
title = {The gut microbiota intervenes in glucose tolerance and inflammation by regulating the biosynthesis of taurodeoxycholic acid and carnosine.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1423662},
pmid = {39206042},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology ; *Carnosine/metabolism ; Male ; *Feces/microbiology ; Glucose Intolerance/metabolism ; Inflammation/metabolism ; Hep G2 Cells ; Metagenomics ; Female ; Middle Aged ; Taurochenodeoxycholic Acid/metabolism/pharmacology ; Hyperglycemia/metabolism ; Neutrophils/metabolism ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/metabolism/genetics ; },
abstract = {OBJECTIVE: This study aims to investigate the pathogenesis of hyperglycemia and its associated vasculopathy using multiomics analyses in diabetes and impaired glucose tolerance, and validate the mechanism using the cell experiments.<br><br>METHODS: In this study, we conducted a comprehensive analysis of the metagenomic sequencing data of diabetes to explore the key genera related to its occurrence. Subsequently, participants diagnosed with impaired glucose tolerance (IGT), and healthy subjects, were recruited for fecal and blood sample collection. The dysbiosis of the gut microbiota (GM) and its associated metabolites were analyzed using 16S rDNA sequencing and liquid chromatograph mass spectrometry, respectively. The regulation of gene and protein expression was evaluated through mRNA sequencing and data-independent acquisition technology, respectively. The specific mechanism by which GM dysbiosis affects hyperglycemia and its related vasculopathy was investigated using real-time qPCR, Western blotting, and enzyme-linked immunosorbent assay techniques in HepG2 cells and neutrophils.<br><br>RESULTS: Based on the published data, the key alterable genera in the GM associated with diabetes were identified as Blautia, Lactobacillus, Bacteroides, Prevotella, Faecalibacterium, Bifidobacterium, Ruminococcus, Clostridium, and Lachnoclostridium. The related metabolic pathways were identified as cholate degradation and L-histidine biosynthesis. Noteworthy, Blautia and Faecalibacterium displayed similar alterations in patients with IGT compared to those observed in patients with diabetes, and the GM metabolites, tauroursodeoxycholic acid (TUDCA) and carnosine (CARN, a downstream metabolite of histidine and alanine) were both found to be decreased, which in turn regulated the expression of proteins in plasma and mRNAs in neutrophils. Subsequent experiments focused on insulin-like growth factor-binding protein 3 and interleukin-6 due to their impact on blood glucose regulation and associated vascular inflammation. Both proteins were found to be suppressed by TUDCA and CARN in HepG2 cells and neutrophils.<br><br>CONCLUSION: Dysbiosis of the GM occurred throughout the entire progression from IGT to diabetes, characterized by an increase in Blautia and a decrease in Faecalibacterium, leading to reduced levels of TUDCA and CARN, which alleviated their inhibition on the expression of insulin-like growth factor-binding protein 3 and interleukin-6, contributing to the development of hyperglycemia and associated vasculopathy.},
}
@article {pmid39205800,
year = {2024},
author = {Zhang, X and Ye, J and Wang, L and Zhang, L and Wang, L and Jin, H},
title = {Nanopore Sequencing Technology: A Reliable Method for Pathogen Diagnosis in Elderly Patients with Community-Acquired Pneumonia.},
journal = {Infection and drug resistance},
volume = {17},
number = {},
pages = {3659-3667},
pmid = {39205800},
issn = {1178-6973},
abstract = {PURPOSE: Next-generation sequencing of the metagenome (mNGS) is gaining traction as a valuable tool for diagnosing infectious diseases. Compared to mNGS, pathogen detection based on Oxford Nanopore Technology further shortens the detection time. This study seeks to assess the efficacy of Nanopore sequencing in identifying pathogens associated with community-acquired pneumonia (CAP) among elderly individuals in China.<br><br>PATIENTS AND METHODS: From January 2023 to June 2023, elderly patients with CAP were prospectively recruited from Hangzhou First People's Hospital. A comprehensive set of clinical data was gathered, and bronchoalveolar lavage (BAL) fluid samples were collected. Concurrently, pathogen identification was performed using conventional microbiological diagnostic methods, Illumina sequencing, and Nanopore sequencing, and the diagnostic efficacy of pathogen detection was compared.<br><br>RESULTS: The study included a total of 29 patients. The diagnostic positivity rates of traditional microbiological detection, Illumina sequencing, and Nanopore sequencing were 24.1%, 51.7%, and 48.3%, respectively. Their diagnostic specificities were 91.7%, 50%, and 75%, respectively. Compared to traditional microbiological detection, both Nanopore and Illumina sequencing showed significantly increased sensitivity. However, Nanopore sequencing exhibited relatively better consistency with the final clinical comprehensive diagnosis, with a Kappa value of 0.574. This outperformed traditional microbiological detection and Illumina sequencing, which had a Kappa value of 0.296 and 0.402, respectively. In addition, Nanopore sequencing required the shortest turnaround time.<br><br>CONCLUSION: Nanopore sequencing technology demonstrates as a reliable and rapid method for detecting pathogens in elderly patients with CAP.},
}
@article {pmid39205247,
year = {2024},
author = {Jansen van Vuren, P and Parry, RH and Pawęska, JT},
title = {Detection of Dengue Virus 1 and Mammalian Orthoreovirus 3, with Novel Reassortments, in a South African Family Returning from Thailand, 2017.},
journal = {Viruses},
volume = {16},
number = {8},
pages = {},
pmid = {39205247},
issn = {1999-4915},
support = {Annual strategic funding for disease surveillance//National Institute for Communicable Diseases/ ; },
mesh = {Animals ; Child ; Female ; Humans ; Male ; Mice ; Middle Aged ; *Dengue/virology/epidemiology ; *Dengue Virus/genetics/isolation &amp; purification/classification ; Genome, Viral ; Genotype ; Orthoreovirus, Mammalian/genetics/isolation &amp; purification/classification ; *Phylogeny ; *Reassortant Viruses/genetics/isolation &amp; purification/classification ; Reoviridae Infections/virology/veterinary ; South Africa ; Thailand ; Travel ; Vero Cells ; },
abstract = {In July 2017, a family of three members, a 46-year-old male, a 45-year-old female and their 8-year-old daughter, returned to South Africa from Thailand. They presented symptoms consistent with mosquito-borne diseases, including fever, headache, severe body aches and nausea. Mosquito bites in all family members suggested recent exposure to arthropod-borne viruses. Dengue virus 1 (Genus Orthoflavivirus) was isolated (isolate no. SA397) from the serum of the 45-year-old female via intracerebral injection in neonatal mice and subsequent passage in VeroE6 cells. Phylogenetic analysis of this strain indicated close genetic identity with cosmopolitan genotype 1 DENV1 strains from Southeast Asia, assigned to major lineage K, minor lineage 1 (DENV1I_K.1), such as GZ8H (99.92%) collected in November 2018 from China, and DV1I-TM19-74 isolate (99.72%) identified in Bangkok, Thailand, in 2019. Serum samples from the 46-year-old male yielded a virus isolate that could not be confirmed as DENV1, prompting unbiased metagenomic sequencing for virus identification and characterization. Illumina sequencing identified multiple segments of a mammalian orthoreovirus (MRV), designated as Human/SA395/SA/2017. Genomic and phylogenetic analyses classified Human/SA395/SA/2017 as MRV-3 and assigned a tentative genotype, MRV-3d, based on the S1 segment. Genomic analyses suggested that Human/SA395/SA/2017 may have originated from reassortments of segments among swine, bat, and human MRVs. The closest identity of the viral attachment protein σ1 (S1) was related to a human isolate identified from Tahiti, French Polynesia, in 1960. This indicates ongoing circulation and co-circulation of Southeast Asian and Polynesian strains, but detailed knowledge is hampered by the limited availability of genomic surveillance. This case represents the rare concurrent detection of two distinct viruses with different transmission routes in the same family with similar clinical presentations. It highlights the complexity of diagnosing diseases with similar sequelae in travelers returning from tropical areas.},
}
@article {pmid39205216,
year = {2024},
author = {Patiño, L and Benítez, AD and Carrazco-Montalvo, A and Regato-Arrata, M},
title = {Genomics for Arbovirus Surveillance: Considerations for Routine Use in Public Health Laboratories.},
journal = {Viruses},
volume = {16},
number = {8},
pages = {},
pmid = {39205216},
issn = {1999-4915},
support = {Proyecto IN&#xc9;DITA-PIC-21-INE-INSPI-001//Secretar&#xed;a de Educaci&#xf3;n Superior, Ciencia, Tecnolog&#xed;a e Innovaci&#xf3;n/ ; },
mesh = {*Arboviruses/genetics/isolation &amp; purification ; *Arbovirus Infections/epidemiology/diagnosis/virology ; Humans ; *Genomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; *Public Health ; Animals ; Laboratories ; Computational Biology/methods ; Genome, Viral ; Epidemiological Monitoring ; },
abstract = {The emergence and re-emergence of arthropod-borne viruses is a public health threat. For routine surveillance in public health laboratories, cost-effective and reproducible methods are essential. In this review, we address the technical considerations of high-throughput sequencing methods (HTS) for arbovirus surveillance in national health laboratories, focusing on pre-sequencing, sequencing, and post-sequencing approaches, underlining the importance of robust wet and dry laboratory workflows for reproducible analysis. We aim to provide insights for researchers and clinicians interested in arbovirus, diagnosis, and surveillance by discussing current advances in sequencing methods and bioinformatics pipelines applied to arboviruses.},
}
@article {pmid39205200,
year = {2024},
author = {Santos, JPN and Rodrigues, GVP and Ferreira, LYM and Monteiro, GP and Fonseca, PLC and Lopes, &#xcd;S and Florêncio, BS and da Silva Junior, AB and Ambrósio, PE and Pirovani, CP and Aguiar, ERGR},
title = {The Virome of Cocoa Fermentation-Associated Microorganisms.},
journal = {Viruses},
volume = {16},
number = {8},
pages = {},
pmid = {39205200},
issn = {1999-4915},
support = {Financial code 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior-Brazil (CAPES)/ ; Researcher fellowship//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (CNPq)/ ; },
mesh = {*Cacao/virology/microbiology ; *Fermentation ; *Virome ; Viruses/genetics/classification/isolation &amp; purification ; Fungi/virology/genetics/classification ; Phylogeny ; Bacteriophages/genetics/classification/isolation &amp; purification ; Costa Rica ; Bacteria/genetics/classification/virology ; Metagenomics ; Genome, Viral ; },
abstract = {Theobroma cacao plantations are of significant economic importance worldwide, primarily for chocolate production. During the harvest and processing of cocoa beans, they are subjected to fermentation either by microorganisms present in the environment (spontaneous fermentation) or the addition of starter cultures, with different strains directly contributing distinct flavor and color characteristics to the beans. In addition to fungi and bacteria, viruses are ubiquitous and can affect the quality of the fermentation process by infecting fermenting organisms, destabilizing microbial diversity, and consequently affecting fermentation quality. Therefore, in this study, we explored publicly available metatranscriptomic libraries of cocoa bean fermentation in Limon Province, Costa Rica, looking for viruses associated with fermenting microorganisms. Libraries were derived from the same sample at different time points: 7, 20, and 68 h of fermentation, corresponding to yeast- and lactic acid bacteria-driven phases. Using a comprehensive pipeline, we identified 68 viral sequences that could be assigned to 62 new viral species and 6 known viruses distributed among at least nine families, with particular abundance of elements from the Lenarviricota phylum. Interestingly, 44 of these sequences were specifically associated with ssRNA phages (Fiersviridae) and mostly fungi-infecting viral families (Botourmiaviridae, Narnaviridae, and Mitoviridae). Of note, viruses from those families show a complex evolutionary relationship, transitioning from infecting bacteria to infecting fungi. We also identified 10 and 3 viruses classified within the Totiviridae and Nodaviridae families, respectively. The quantification of the virus-derived RNAs shows a general pattern of decline, similar to the dynamic profile of some microorganism genera during the fermentation process. Unexpectedly, we identified narnavirus-related elements that showed similarity to segmented viral species. By exploring the molecular characteristics of these viral sequences and applying Hidden Markov Models, we were capable of associating these additional segments with a specific taxon. In summary, our study elucidates the complex virome associated with the microbial consortia engaged in cocoa bean fermentation that could contribute to organism/strain selection, altering metabolite production and, consequently, affecting the sensory characteristics of cocoa beans.},
}
@article {pmid39204265,
year = {2024},
author = {Ariyadasa, S and van Hamelsveld, S and Taylor, W and Lin, S and Sitthirit, P and Pang, L and Billington, C and Weaver, L},
title = {Diversity of Free-Living Amoebae in New Zealand Groundwater and Their Ability to Feed on Legionella pneumophila.},
journal = {Pathogens (Basel, Switzerland)},
volume = {13},
number = {8},
pages = {},
pmid = {39204265},
issn = {2076-0817},
support = {ESR2023SA1//Ministry of Business, Innovation, and Employment New Zealand/ ; },
abstract = {Free-living amoebae (FLA) are common in both natural and engineered freshwater ecosystems. They play important roles in biofilm control and contaminant removal through the predation of bacteria and other taxa. Bacterial predation by FLA is also thought to contribute to pathogen dispersal and infectious disease transmission in freshwater environments via the egestion of viable bacteria. Despite their importance in shaping freshwater microbial communities, the diversity and function of FLA in many freshwater ecosystems are poorly understood. In this study, we isolated and characterized FLA from two groundwater sites in Canterbury, New Zealand using microbiological, microscopic, and molecular techniques. Different methods for groundwater FLA isolation and enrichment were trialed and optimized. The ability of these isolated FLA to predate on human pathogen Legionella pneumophila was assessed. FLA were identified by 18S metagenomic amplicon sequencing. Our study showed that Acanthamoeba spp. (including A. polyphaga) and Vermamoeba veriformis were the main FLA species present in both groundwater sites examined. While most of the isolated FLA co-existed with L. pneumophila, the FLA populations in the L. pneumophila co-culture experiments predominantly consisted of A. polyphaga, Acanthamoeba spp., Naegleria spp., V. vermiformis, Paravahlkampfia spp., and Echinamoeba spp. These observations suggest that FLA may have the potential to act as reservoirs for L. pneumophila in Canterbury, New Zealand groundwater systems and could be introduced into the local drinking water infrastructure, where they may promote the survival, multiplication, and dissemination of Legionella. This research addresses an important gap in our understanding of FLA-mediated pathogen dispersal in freshwater ecosystems.},
}
@article {pmid39204226,
year = {2024},
author = {Kibenge, F and Kibenge, M and Montes de Oca, M and Godoy, M},
title = {Parvoviruses of Aquatic Animals.},
journal = {Pathogens (Basel, Switzerland)},
volume = {13},
number = {8},
pages = {},
pmid = {39204226},
issn = {2076-0817},
abstract = {Family Parvoviridae consists of small, non-enveloped viruses with linear, single-stranded DNA genomes of approximately 4-6 kilobases, subdivided into three subfamilies, Parvovirinae, Densovirinae, and Hamaparvovirinae, and unassigned genus Metalloincertoparvovirus. Parvoviruses of aquatic animals infect crustaceans, mollusks, and finfish. This review describes these parvoviruses, which are highly host-specific and associated with mass morbidity and mortality in both farmed and wild aquatic animals. They include Cherax quadricarinatus densovirus (CqDV) in freshwater crayfish in Queensland, Australia; sea star-associated densovirus (SSaDV) in sunflower sea star on the Northeastern Pacific Coast; Clinch densovirus 1 in freshwater mussels in the Clinch River, Virginia, and Tennessee, USA, in subfamily Densovirinae; hepatopancreatic parvovirus (HPV) and infectious hypodermal and hematopoietic necrosis virus (IHHNV) in farmed shrimp worldwide; Syngnathid ichthamaparvovirus 1 in gulf pipefish in the Gulf of Mexico and parts of South America; tilapia parvovirus (TiPV) in farmed tilapia in China, Thailand, and India, in the subfamily Hamaparvovirinae; and Penaeus monodon metallodensovirus (PmMDV) in Vietnamese P. monodon, in unassigned genus Metalloincertoparvovirus. Also included in the family Parvoviridae are novel parvoviruses detected in both diseased and healthy animals using metagenomic sequencing, such as zander parvovirus from zander in Hungary and salmon parvovirus from sockeye salmon smolts in British Columbia, Canada.},
}
@article {pmid39204040,
year = {2024},
author = {Zhang, LN and Tan, JT and Ng, HY and Liao, YS and Zhang, RQ and Chan, KH and Hung, IF and Lam, TT and Cheung, KS},
title = {Baseline Gut Microbiota Was Associated with Long-Term Immune Response at One Year Following Three Doses of BNT162b2.},
journal = {Vaccines},
volume = {12},
number = {8},
pages = {},
pmid = {39204040},
issn = {2076-393X},
support = {COVID1903010//Food and Health Bureau, The Government of HKSAR/ ; },
abstract = {BACKGROUND: This study explored neutralizing IgG antibody levels against COVID-19 decline over time post-vaccination. We conducted this prospective cohort study to investigate the function of gut microbiota in the host immune response following three doses of BNT162b2.<br><br>METHODS: Subjects who received three doses of BNT162b2 were recruited from three centers in Hong Kong. Blood samples were obtained before the first dose and at the one-year timepoint for IgG ELISA to determine the level of neutralizing antibody (NAb). The primary outcome was a high immune response (NAb > 600 AU/mL). We performed shotgun DNA metagenomic sequencing on baseline fecal samples to identify bacterial species and metabolic pathways associated with high immune response using linear discriminant analysis effect size analysis.<br><br>RESULTS: A total of 125 subjects were recruited (median age: 52 years [IQR: 46.2-59.0]; male: 43 [34.4%]), and 20 were regarded as low responders at the one-year timepoint. Streptococcus parasanguinis (log10LDA score = 2.38, p = 0.003; relative abundance of 2.97 &#xd7; 10[-5] vs. 0.03%, p = 0.001), Bacteroides stercoris (log10LDA score = 4.29, p = 0.024; relative abundance of 0.14% vs. 2.40%, p = 0.014) and Haemophilus parainfluenzae (log10LDA score = 2.15, p = 0.022; relative abundance of 0.01% vs. 0, p = 0.010) were enriched in low responders. Bifidobacterium pseudocatenulatum (log10LDA score = 2.99, p = 0.048; relative abundance of 0.09% vs. 0.36%, p = 0.049) and Clostridium leptum (log10LDA score = 2.38, p = 0.014; relative abundance of 1.2 &#xd7; 10[-5]% vs. 0, p = 0.044) were enriched in high responders. S. parasanguinis was negatively correlated with the superpathway of pyrimidine ribonucleotides de novo biosynthesis (log10LDA score = 2.63), which contributes to inflammation and antibody production. H. parainfluenzae was positively correlated with pathways related to anti-inflammatory processes, including the superpathway of histidine, purine, and pyrimidine biosynthesis (log10LDA score = 2.14).<br><br>CONCLUSION: Among three-dose BNT162b2 recipients, S. parasanguinis, B. stercoris and H. parainfluenzae were associated with poorer immunogenicity at one year, while B. pseudocatenulatum and C. leptum was associated with a better response.},
}
@article {pmid39203557,
year = {2024},
author = {Gaenssle, ALO and Bertran-Llorens, S and Deuss, PJ and Jurak, E},
title = {Enrichment of Aquatic Xylan-Degrading Microbial Communities.},
journal = {Microorganisms},
volume = {12},
number = {8},
pages = {},
pmid = {39203557},
issn = {2076-2607},
support = {ENTEG//University of Groningen (ENTEG)/ ; },
abstract = {The transition towards a sustainable society involves the utilization of lignocellulosic biomass as a renewable feedstock for materials, fuel, and base chemicals. Lignocellulose consists of cellulose, hemicellulose, and lignin, forming a complex, recalcitrant matrix where efficient enzymatic saccharification is pivotal for accessing its valuable components. This study investigated microbial communities from brackish Lauwersmeer Lake, in The Netherlands, as a potential source of xylan-degrading enzymes. Environmental sediment samples were enriched with wheat arabinoxylan (WAX) and beechwood glucuronoxylan (BEX), with enrichment on WAX showing higher bacterial growth and complete xylan degradation compared to BEX. Metagenomic sequencing revealed communities consisting almost entirely of bacteria (>99%) and substantial shifts in composition during the enrichment. The first generation of seven-day enrichments on both xylans led to a high accumulation of Gammaproteobacteria (49% WAX, 84% BEX), which were largely replaced by Alphaproteobacteria (42% WAX, 69% BEX) in the fourth generation. Analysis of the protein function within the sequenced genomes showed elevated levels of genes associated with the carbohydrate catabolic process, specifically targeting arabinose, xylose, and xylan, indicating an adaptation to the primary monosaccharides present in the carbon source. The data open up the possibility of discovering novel xylan-degrading proteins from other sources aside from the thoroughly studied Bacteroidota.},
}
@article {pmid39203545,
year = {2024},
author = {Gheorghe-Barbu, I and Dragomir, RI and Gradisteanu Pircalabioru, G and Surleac, M and Dinu, IA and Gaboreanu, MD and Czobor Barbu, I},
title = {Tracing Acinetobacter baumannii's Journey from Hospitals to Aquatic Ecosystems.},
journal = {Microorganisms},
volume = {12},
number = {8},
pages = {},
pmid = {39203545},
issn = {2076-2607},
support = {ERANET 243/2021//ERANET/ ; PN-III-P4-PCE-2021-1797 (PCE 96/2022)//Unitatea Executiva Pentru Finantarea Invatamantului Superior a Cercetarii Dezvoltarii si Inovarii/ ; PN-III-P1-1.1-TE-2021-1515 (TE112/2022)//Unitatea Executiva Pentru Finantarea Invatamantului Superior a Cercetarii Dezvoltarii si Inovarii/ ; PN-III-P1-1.1-PD-2021-0540 (PD102/2022)//Unitatea Executiva Pentru Finantarea Invatamantului Superior a Cercetarii Dezvoltarii si Inovarii/ ; },
abstract = {BACKGROUND: This study provides a comprehensive analysis of Acinetobacter baumannii in aquatic environments and fish microbiota by integrating culture-dependent methods, 16S metagenomics, and antibiotic resistance profiling.<br><br>METHODS: A total of 83 A. baumannii isolates were recovered using culture-dependent methods from intra-hospital infections (IHI) and wastewater (WW) and surface water (SW) samples from two southern Romanian cities in August 2022. The antibiotic susceptibility was screened using disc diffusion, microdilution, PCR, and Whole Genome Sequencing assays.<br><br>RESULTS: The highest microbial load in the analyzed samples was found in Glina, Bucharest, for both WW and SW samples across all investigated phenotypes. For Bucharest isolates, the resistance levels corresponded to fluoroquinolones > aminoglycosides > &#x3b2;-lactam antibiotics. In contrast, A. baumannii from upstream SW samples in T&#xe2;rgovi&#x219;te showed the highest resistance to aminoglycosides. The blaOXA-23 gene was frequently detected in IHI, WW, and SW isolates in Bucharest, but was absent in T&#xe2;rgovi&#x219;te. Molecular phylogeny revealed the presence of ST10 in T&#xe2;rgovi&#x219;te isolates and ST2 in Bucharest isolates, while other minor STs were not specifically correlated with a sampling point. Using 16S rRNA sequencing, significant differences in microbial populations between the two locations was identified. The low abundance of Alphaproteobacteria and Actinobacteria in both locations suggests environmental pressures or contamination events.<br><br>CONCLUSIONS: These findings indicate significant fecal contamination and potential public health risks, emphasizing the need for improved water quality monitoring and management.},
}
@article {pmid39203533,
year = {2024},
author = {Chiba, T and Hattori, Y and Motooka, D and Tanaka, T and Ihara, M},
title = {Paraclostridium tenue Causing an Anaerobic Brain Abscess Identified by Whole-Metagenome Sequencing: A Case Report.},
journal = {Microorganisms},
volume = {12},
number = {8},
pages = {},
pmid = {39203533},
issn = {2076-2607},
support = {N/A//Nature Holdings/ ; },
abstract = {When treating anaerobic brain abscesses, healthcare professionals often face the difficulty of identifying the causal pathogens, necessitating empiric therapies with uncertain efficacy. We present the case of a 57-year-old woman who was admitted to our hospital with a fever and headache. Brain magnetic resonance imaging revealed a hemorrhagic lesion with wall enhancement at the left hemisphere on contrast-enhanced T1-weighted imaging. Cerebrospinal fluid examination showed pleocytosis (23 cells/μL), an elevated protein level (125 mg/dL), and decreased glucose level (51 mg/dL; blood glucose was 128 mg/dL). Intracerebral hemorrhage accompanied by a brain abscess was clinically suspected. The patient received empirical treatment with intravenous meropenem and vancomycin for 2 weeks. However, conventional bacterial culture tests failed to identify the pathogen. We then performed shotgun sequencing and ribosomal multilocus sequence typing, which identified Paraclostridium tenue. Based on this finding, we de-escalated to benzylpenicillin potassium for 4 weeks, leading to a 2.5-year remission of the anaerobic brain abscess. Therefore, Paraclostridium can be a causative pathogen for brain abscesses. Furthermore, whole-metagenome sequencing is a promising method for detecting rare pathogens that are not identifiable by conventional bacterial culture tests. This approach enables more targeted treatment and contributes to achieving long-term remission in clinical settings.},
}
@article {pmid39203491,
year = {2024},
author = {Zhang, R and Wang, S and Zhong, H and Fu, X and Li, L and Wang, L and Liu, Y},
title = {Microbial C and N Metabolism Alterations Based on Soil Metagenome and Different Shrub Invasion Stages in Sanjiang Plain Wetlands.},
journal = {Microorganisms},
volume = {12},
number = {8},
pages = {},
pmid = {39203491},
issn = {2076-2607},
support = {HC202332//Open Project of State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology/ ; },
abstract = {Shrub invasion affects plant growth and soil physicochemical properties, resulting in soil microbiota metabolic pathway changes. However, little is known about the shrub expansion intensity of microbial metabolic pathway processes. In this study, we used metagenome sequencing technology to investigate changes in soil microbial C and N metabolic pathways and community structures, along with different shrub invasion intensities, in the Sanjiang Plain wetlands. Different shrub invasion intensities significantly affected the soil microbial composition (β diversity), with no significant effect on the α diversity compared to CK. AN, pH, and TP were the major factors influencing the microbial community's structures. Compared to CK, the shrub expansion intensity did not significantly affect C fixation and central metabolism but significantly reduced methanogenesis, which involves the CO2-to-methane transition that occurs in methane metabolism, and denitrification, the nitrite to nitric oxide (nirK or nirS) transition that occurs in N metabolism. This study provides an in-depth understanding of the biogeochemical cycles of wetland ecosystems in cold northern regions undergoing shrub invasion.},
}
@article {pmid39203451,
year = {2024},
author = {Onyeaghala, GC and Sharma, S and Oyenuga, M and Staley, CM and Milne, GL and Demmer, RT and Shaukat, A and Thyagarajan, B and Straka, RJ and Church, TR and Prizment, AE},
title = {The Effects of Aspirin Intervention on Inflammation-Associated Lingual Bacteria: A Pilot Study from a Randomized Clinical Trial.},
journal = {Microorganisms},
volume = {12},
number = {8},
pages = {},
pmid = {39203451},
issn = {2076-2607},
support = {UL1 TR002494/TR/NCATS NIH HHS/United States ; UL1TR002494//National Institutes of Health's National Center for Advancing Translational Sciences/ ; },
abstract = {Several bacterial taxa enriched in inflammatory bowel diseases and colorectal cancer (CRC) are found in the oral cavity. We conducted a pilot study nested within a six-week aspirin intervention in a randomized placebo-controlled trial to test their response to aspirin intervention. Fifty healthy subjects, 50-75 years old, were randomized to receive 325 mg aspirin (n = 30) or placebo (n = 20) orally once daily for six weeks. Oral tongue swabs were collected at baseline and week six. We estimated the association between aspirin use and the temporal changes in the relative abundance of pre-specified genus level taxa from pre- to post-treatment. The temporal change in relative abundance differed for eight genus level taxa between the aspirin and placebo groups. In the aspirin group, there were significant increases in the relative abundances of Neisseria, Streptococcus, Actinomyces, and Rothia and significant decreases in Prevotella, Veillonella, Fusobacterium, and Porphyromonas relative to placebo. The log ratio of Neisseria to Fusobacterium declined more in the aspirin group than placebo, signaling a potential marker associated with aspirin intervention. These preliminary findings should be validated using metagenomic sequencing and may guide future studies on the role of aspirin on taxa in various oral ecological niches.},
}
@article {pmid39203445,
year = {2024},
author = {Pomari, E and Orza, P and Bernardi, M and Fracchetti, F and Campedelli, I and De Marta, P and Recchia, A and Paradies, P and Buonfrate, D},
title = {A Pilot Study for the Characterization of Bacillus spp. and Analysis of Possible B. thuringiensis/Strongyloides stercoralis Correlation.},
journal = {Microorganisms},
volume = {12},
number = {8},
pages = {},
pmid = {39203445},
issn = {2076-2607},
support = {"5&#xd7;1000 -2020", project: "Bacillus thuringiensis (gruppo Bacillus cereus) come possibile antagonista di Strongyloides stercoralis e di altri elminti correlati con malattie tropicali neglette (NTD), alla base di una strategia di prevenzione"//Italian Ministry of Health/ ; "Ricerca Corrente", project L2P11//Italian Ministry of Health/ ; },
abstract = {Differentiating between Bacillus species is relevant in human medicine. Bacillus thuringiensis toxins might be effective against Strongyloides stercoralis, a nematode causing relevant human morbidity. Our first objective was to evaluate genomic and MALDI-TOF identification methods for B. thuringiensis. Our secondary objective was to evaluate a possible negative selection pressure of B. thuringiensis against S. stercoralis. PCR and Sanger were compared to MALDI-TOF on a collection of 44 B. cereus group strains. B. thuringiensis toxin genes were searched on 17 stool samples from S. stercoralis-infected and uninfected dogs. Metagenomic 16S rRNA was used for microbiome composition. The inter-rate agreement between PCR, Sanger, and MALDI-TOF was 0.631 k (p-value = 6.4 × 10[-10]). B. thuringiensis toxins were not found in dogs' stool. Bacteroidota and Bacillota were the major phyla in the dogs' microbiome (both represented >20% of the total bacterial community). Prevotella was underrepresented in all Strongyloides-positive dogs. However, the general composition of bacterial communities was not significantly linked with S. stercoralis infection. The genomic methods allowed accurate differentiation between B. thuringiensis and B. cereus. There was no association between B. thuringiensis and S. stercoralis infection, but further studies are needed to confirm this finding. We provide the first descriptive results about bacterial fecal composition in dogs with S. stercoralis infection.},
}
@article {pmid39203436,
year = {2024},
author = {Majeed, A and Liu, J and Knight, AJ and Pajerowska-Mukhtar, KM and Mukhtar, MS},
title = {Bacterial Communities Associated with the Leaves and the Roots of Salt Marsh Plants of Bayfront Beach, Mobile, Alabama, USA.},
journal = {Microorganisms},
volume = {12},
number = {8},
pages = {},
pmid = {39203436},
issn = {2076-2607},
support = {IOS-2038872//National Science Foundation/ ; },
abstract = {Salt marshes are highly dynamic and biologically diverse ecosystems that serve as natural habitats for numerous salt-tolerant plants (halophytes). We investigated the bacterial communities associated with the roots and leaves of plants growing in the coastal salt marshes of the Bayfront Beach, located in Mobile, Alabama, United States. We compared external (epiphytic) and internal (endophytic) communities of both leaf and root plant organs. Using 16S rDNA amplicon sequencing methods, we identified 10 bacterial phyla and 59 different amplicon sequence variants (ASVs) at the genus level. Bacterial strains belonging to the phyla Proteobacteria, Bacteroidetes, and Firmicutes were highly abundant in both leaf and root samples. At the genus level, sequences of the genus Pseudomonas were common across all four sample types, with the highest abundance found in the leaf endophytic community. Additionally, Pantoea was found to be dominant in leaf tissue compared to roots. Our study revealed that plant habitat (internal vs. external for leaves and roots) was a determinant of the bacterial community structure. Co-occurrence network analyses enabled us to discern the intricate characteristics of bacterial taxa. Our network analysis revealed varied levels of ASV complexity in the epiphytic networks of roots and leaves compared to the endophytic networks. Overall, this study advances our understanding of the intricate composition of the bacterial microbiota in habitats (epiphytic and endophytic) and organs (leaf and root) of coastal salt marsh plants and suggests that plants might recruit habitat- and organ-specific bacteria to enhance their tolerance to salt stress.},
}
@article {pmid39203404,
year = {2024},
author = {Corrigan, A and McCooey, P and Taylor-Pickard, J and Stockdale, S and Murphy, R},
title = {Breaking the Cycle: A Yeast Mannan-Rich Fraction Beneficially Modulates Egg Quality and the Antimicrobial Resistome Associated with Layer Hen Caecal Microbiomes under Commercial Conditions.},
journal = {Microorganisms},
volume = {12},
number = {8},
pages = {},
pmid = {39203404},
issn = {2076-2607},
abstract = {Antibiotics and antibiotic growth promoters have been extensively employed in poultry farming to enhance growth performance, maintain bird health, improve nutrient uptake efficiency, and mitigate enteric diseases at both sub-therapeutic and therapeutic doses. However, the extensive use of antimicrobials in poultry farming has led to the emergence of antimicrobial resistance (AMR) in microbial reservoirs, representing a significant global public health concern. In response, non-antibiotic dietary interventions, such as yeast mannan-rich fraction (MRF), have emerged as a promising alternative to modulate the gut microbiota and combat the AMR crisis. This study investigated whether a yeast mannan-rich fraction containing feed supplement impacted the performance of laying hens, their microbiomes, and the associated carriage of antimicrobial resistance genes under commercial conditions. High-throughput DNA sequencing was utilised to profile the bacterial community and assess changes in the antibiotic resistance genomes detected in the metagenome, the "resistome", in response to MRF supplementation. It was found that supplementation favourably influenced laying hen performance and microbial composition. Notably, there was a compositional shift in the MRF supplemented group associated with a lower relative abundance of pathobionts, e.g., Escherichia, Brachyspira and Trueperella, and their AMR-encoded genes, relative to beneficial microbes. Overall, the findings further demonstrate the ability of prebiotics to improve laying hen performance through changes associated with their microbiome and resistome.},
}
@article {pmid39203393,
year = {2024},
author = {Wang, Y and Weng, MY and Zhong, JW and He, L and Guo, DJ and Luo, D and Xue, JY},
title = {Microbial Metagenomics Revealed the Diversity and Distribution Characteristics of Groundwater Microorganisms in the Middle and Lower Reaches of the Yangtze River Basin.},
journal = {Microorganisms},
volume = {12},
number = {8},
pages = {},
pmid = {39203393},
issn = {2076-2607},
support = {SWJ-CJX23Z11//the 2023 Science and Technology Innovation Fund Project of Hydrology Bureau of Yangtze River Water Resources Commission/ ; },
abstract = {Groundwater is one of the important freshwater resources on Earth and is closely related to human activities. As a good biological vector, a more diverse repertory of antibiotic resistance genes in the water environment would have a profound impact on human medical health. Therefore, this study conducted a metagenomic sequencing analysis of water samples from groundwater monitoring points in the middle and lower reaches of the Yangtze River to characterize microbial community composition and antibiotic resistance in the groundwater environment. Our results show that different microbial communities and community composition were the driving factors in the groundwater environment, and a diversity of antibiotic resistance genes in the groundwater environment was detected. The main source of antibiotic resistance gene host was determined by correlation tests and analyses. In this study, metagenomics was used for the first time to comprehensively analyze microbial communities in groundwater systems in the middle and lower reaches of the Yangtze River basin. The data obtained from this study serve as an invaluable resource and represent the basic metagenomic characteristics of groundwater microbial communities in the middle and lower reaches of the Yangtze River basin. These findings will be useful tools and provide a basis for future research on water microbial community and quality, greatly expanding the depth and breadth of our understanding of groundwater.},
}
@article {pmid39203351,
year = {2024},
author = {Liang, J and Zheng, X and Ning, T and Wang, J and Wei, X and Tan, L and Shen, F},
title = {Revealing the Viable Microbial Community of Biofilm in a Sewage Treatment System Using Propidium Monoazide Combined with Real-Time PCR and Metagenomics.},
journal = {Microorganisms},
volume = {12},
number = {8},
pages = {},
pmid = {39203351},
issn = {2076-2607},
support = {42307051//National Natural Science Foundation of China/ ; 2022M713416//China Postdoctoral Science Foundation/ ; CAAS-ZDRW202306//Special Fund for Basic Scientific Research of Central Public Welfare Institutes/ ; },
abstract = {Microbial community composition, function, and viability are important for biofilm-based sewage treatment technologies. Most studies of microbial communities mainly rely on the total deoxyribonucleic acid (DNA) extracted from the biofilm. However, nucleotide materials released from dead microorganisms may interfere with the analysis of viable microorganisms and their metabolic potential. In this study, we developed a protocol to assess viability as well as viable community composition and function in biofilm in a sewage treatment system using propidium monoazide (PMA) coupled with real-time quantitative polymerase chain reaction (qPCR) and metagenomic technology. The optimal removal of PMA from non-viable cells was achieved by a PMA concentration of 4 μM, incubation in darkness for 5 min, and exposure for 5 min. Simultaneously, the detection limit can reach a viable bacteria proportion of 1%, within the detection concentration range of 10[2]-10[8] CFU/mL (colony forming unit/mL), showing its effectiveness in removing interference from dead cells. Under the optimal conditions, the result of PMA-metagenomic sequencing revealed that 6.72% to 8.18% of non-viable microorganisms were influenced and the composition and relative abundance of the dominant genera were changed. Overall, this study established a fast, sensitive, and highly specific biofilm viability detection method, which could provide technical support for accurately deciphering the structural composition and function of viable microbial communities in sewage treatment biofilms.},
}
@article {pmid39202671,
year = {2024},
author = {Jalal, RS and Sonbol, HS},
title = {Resistome Signature and Antibiotic Resistance Mechanisms in Rhizospheric Soil Bacteriomes of Mecca Region, Saudi Arabia: Insights into Impact on Human Health.},
journal = {Life (Basel, Switzerland)},
volume = {14},
number = {8},
pages = {},
pmid = {39202671},
issn = {2075-1729},
support = {PNURSP2024R83//Princess Nourah bint Abdulrahman University/ ; },
abstract = {The objective of this investigation is to ascertain the distinctive profile of the rhizospheric soil resistome within the Mecca region, while also evaluating the potential risks associated with the horizontal transfer of resistome determinants to the open environment and human clinical isolates. We have made metagenomic whole-genome shotgun sequencing for rhizospheric microbiomes of two endemic plants, namely Moringa oleifera and Abutilon fruticosum. The rhizospheric resistomes of the two plants and the abundance of antibiotic resistance genes (ARGs) were identified by cross-referencing encoded proteins with the comprehensive antibiotic resistance database (CARD). The identified ARGs were then analyzed for their antimicrobial resistance (AMR) mechanisms. Predominantly within this soil are the two bacterial species Pseudomonas aeruginosa and Mycobacterium tuberculosis. These opportunistic human pathogens are implicated in respiratory infections and are correlated with heightened mortality rates. The most prevalent array of ARGs existing in this soil comprises mexA, mexC, mexE, and cpxR, associated with mechanisms of antibiotic active efflux, along with ACC(2), ACC(3), AAC(6), and APH(6), in addition to arr1, arr3, arr4, iri, rphA, and rphB, implicated in antibiotic inactivation. Furthermore, vanS, vanR, and vanJ are identified for antibiotic target alteration, while rpoB2 and RbpA are noted for antibiotic target replacement and protection, respectively. These mechanisms confer resistance against a diverse spectrum of drug classes encompassing fluoroquinolones, aminoglycosides, glycopeptides, and rifampicins. This study underscores the potential hazards posed to human health by the presence of these pathogenic bacteria within the rhizospheric soil of the Mecca region, particularly in scenarios where novel ARGs prevalent in human populations are harbored and subsequently transmitted through the food chain to human clinical isolates. Consequently, stringent adherence to good agricultural and food transportation practices is imperative, particularly with regard to edible plant parts and those utilized in folkloric medicine.},
}
@article {pmid39202448,
year = {2024},
author = {Minelli, M and Anaclerio, F and Calisi, D and Onofrj, M and Antonucci, I and Gatta, V and Stuppia, L},
title = {Application of Metagenomics Sequencing in a Patient with Dementia: A New Case Report.},
journal = {Genes},
volume = {15},
number = {8},
pages = {},
pmid = {39202448},
issn = {2073-4425},
mesh = {Humans ; *Dementia/genetics/microbiology ; *Metagenomics/methods ; *RNA, Ribosomal, 16S/genetics ; Male ; Aged ; High-Throughput Nucleotide Sequencing/methods ; Female ; DNA, Bacterial/genetics ; },
abstract = {(1) Background: The study of the microbiome is crucial for its role in major systemic diseases, in particular the oral and gut microbiota. In recent years, the study of microorganisms correlated, for example, with neurodegenerative disease has increased the prospect of a possible link between gut microbiota and the brain. Here, we report a new case concerning a patient who was initially evaluated genetically for dementia and late-onset dyskinesia, and later tested with 16S metagenomics sequencing. (2) Methods: Starting from a buccal swab, we extracted bacterial DNA and then we performed NGS metagenomics sequencing based on the amplification of the hypervariable regions of the 16S rRNA gene in bacteria. (3) Results: The sequencing revealed the presence of the Spirochaetes phylum, a pathogenic bacterium generally known to be capable of migrating to the Central Nervous System. (4) Conclusions: Oral infections, as our results suggest, could be possible contributing factors to various neurodegenerative conditions.},
}
@article {pmid39202441,
year = {2024},
author = {Li, L and Miao, W and Li, Z and Huang, L and Hau, E and Khan, MF and Liu, Q and Zeng, Q and Cui, K},
title = {Meta-Genomic Analysis of Different Bacteria and Their Genomes Found in Raw Buffalo Milk Obtained in Various Farms Using Different Milking Methods.},
journal = {Genes},
volume = {15},
number = {8},
pages = {},
pmid = {39202441},
issn = {2073-4425},
support = {No. AA22068099//Guangxi Science and Technology Department/ ; No. nycytxgxcxtd-2021-21-02//Guangxi Innovation Team Construction of National Modern Agricultural Industrial Tech-nology System/ ; },
mesh = {Animals ; *Milk/microbiology ; *Buffaloes/microbiology ; Bacteria/genetics/classification/isolation &amp; purification ; Female ; Dairying/methods ; Genome, Bacterial ; Farms ; China ; Metagenomics/methods ; Staphylococcus/genetics/isolation &amp; purification ; },
abstract = {Milking methods have significant impacts on the microbiological composition, which could affect the quality of raw buffalo milk. Hence, the current study was conducted on the impact of milking methods on microorganisms in buffalo tank raw milk from 15 farms in Guangxi, China. The farms were divided into two groups based on the milking method: mechanical milking (MM, n = 6) and hand milking (HM, n = 9). Somatic cell counts, bacterial cell counts and nutrients of the raw buffalo milk samples were analyzed. The comparison of raw buffalo milk samples was analyzed using metagenomic sequencing to detect any differences between the two groups. There was no significant difference in the basic nutritional compositions and somatic cell count of raw buffalo milk between the two milking methods. However, the HM samples had significantly higher bacterial counts and diversity compared to the MM samples. The results showed that Staphylococcus spp., Klebsiella spp., Streptococcus spp., and Pseudomonas spp. were the major microbes present in canned raw buffalo milk. However, the differences between the two milking methods were the relative abundance of core microorganisms and their potential mastitis-causing genera, including the content of antibiotic-resistance genes and virulence genes. Our study revealed that Staphylococcus spp. and Streptococcus spp. were significantly more abundant in the MM group, while Klebsiella spp. was more abundant in the HM group. Regardless of the milking method used, Pseudomonas spp. was identified as the primary genus contributing to antibiotic resistance and virulence genes in canned raw buffalo milk. These findings affirm that there are differences in the microbial and genomic levels in canned raw milk. To prove the functional roles of the discovered genes and how these genes affect milk quality, further research and experimental validation are necessary.},
}
@article {pmid39202331,
year = {2024},
author = {Zheng, X and Xu, L and Tang, Q and Shi, K and Wang, Z and Shi, L and Ding, Y and Yin, Z and Zhang, X},
title = {Integrated Metagenomic and Metabolomics Profiling Reveals Key Gut Microbiota and Metabolites Associated with Weaning Stress in Piglets.},
journal = {Genes},
volume = {15},
number = {8},
pages = {},
pmid = {39202331},
issn = {2073-4425},
support = {202103a06020013//Major special science and technology project of Anhui Province/ ; GXXT-2023-059//the Cooperative Innovation Project of Anhui Provincial Universities/ ; 340000211260001000431//the Joint Research Project on Local Pig Breeding in Anhui Province/ ; 2021YFD1301200//National Key research and development Program of China/ ; },
mesh = {Animals ; *Weaning ; *Gastrointestinal Microbiome ; Swine ; *Metabolomics/methods ; *Metagenomics/methods ; Stress, Physiological ; Metabolome ; Animals, Newborn ; Cecum/microbiology/metabolism ; },
abstract = {(1) Background: Weaning is a challenging and stressful event in the pig's life, which disrupts physiological balance and induces oxidative stress. Microbiota play a significant role during the weaning process in piglets. Therefore, this study aimed to investigate key gut microbiota and metabolites associated with weaning stress in piglets. (2) Methods: A total of ten newborn piglet littermates were randomly assigned to two groups: S (suckling normally) and W (weaned at 21 d; all euthanized at 23 d). Specimens of the cecum were dehydrated with ethanol, cleared with xylene, embedded in paraffin, and cut into 4 mm thick serial sections. After deparaffinization, the sections were stained with hematoxylin and eosin (H&amp;E) for morphometric analysis. Cecal metagenomic and liver LC-MS-based metabolomics were employed in this study. Statistical comparisons were performed by a two-tailed Student's t-test, and p < 0.05 indicated statistical significance. (3) Results: The results showed that weaning led to intestinal morphological damage in piglets. The intestinal villi of suckling piglets were intact, closely arranged in an orderly manner, and finger-shaped, with clear contours of columnar epithelial cells. In contrast, the intestines of weaned piglets showed villous atrophy and shedding, as well as mucosal bleeding. Metagenomics and metabolomics analyses showed significant differences in composition and function between suckling and weaned piglets. The W piglets showed a decrease and increase in the relative abundance of Bacteroidetes and Proteobacteria (p < 0.05), respectively. The core cecal flora in W piglets were Campylobacter and Clostridium, while those in S piglets were Prevotella and Lactobacillus. At the phylum level, the relative abundance of Bacteroidetes significantly decreased (p < 0.05) in weaned piglets, while Proteobacteria significantly increased (p < 0.05). Significant inter-group differences were observed in pathways and glycoside hydrolases in databases, such as the KEGG and CAZymes, including fructose and mannose metabolism, salmonella infection, antifolate resistance, GH135, GH16, GH32, and GH84. We identified 757 differential metabolites between the groups through metabolomic analyses-350 upregulated and 407 downregulated (screened in positive ion mode). In negative ion mode, 541 differential metabolites were identified, with 270 upregulated and 271 downregulated. Major differential metabolites included glycerophospholipids, histidine, nitrogen metabolism, glycine, serine, threonine, β-alanine, and primary bile acid biosynthesis. The significant differences in glycine, serine, and threonine metabolites may be potentially related to dysbiosis caused by weaning stress. Taken together, the identification of microbiome and metabolome signatures of suckling and weaned piglets has paved the way for developing health-promoting nutritional strategies, focusing on enhancing bacterial metabolite production in early life stages.},
}
@article {pmid39201814,
year = {2024},
author = {Gillani, SW and Teng, L and Khan, A and Xu, Y and Powell, CA and Zhang, M},
title = {Fungal Diversity and Gibberellin Hormones Associated with Long Whips of Smut-Infected Sugarcanes.},
journal = {International journal of molecular sciences},
volume = {25},
number = {16},
pages = {},
pmid = {39201814},
issn = {1422-0067},
support = {CARS 170109//China Agricultural Research System/ ; Guike AA22117001//Guangxi Scientific and Technological Department/ ; },
mesh = {*Gibberellins/metabolism ; *Saccharum/microbiology/metabolism ; *Plant Diseases/microbiology ; Fusarium/metabolism/genetics/pathogenicity ; Plant Growth Regulators/metabolism ; Metagenomics/methods ; },
abstract = {Sugarcane smut, caused by the fungus Sporisorium scitamineum (Sydow), significantly affects sugarcane crops worldwide. Infected plants develop whip-like structures known as sori. Significant variations in these whip lengths are commonly observed, but the physiological and molecular differences causing these morphological differences remain poorly documented. To address this, we employed conventional microbe isolation, metagenomic, and metabolomic techniques to investigate smut-infected sugarcane stems and whips of varying lengths. Metagenomics analysis revealed a diverse fungal community in the sugarcane whips, with Sporisorium and Fusarium genera notably present (>1%) in long whips. Isolation techniques confirmed these findings. Ultra-performance liquid chromatography analysis (UHPLC-MS/MS) showed high levels of gibberellin hormones (GA3, GA1, GA4, GA8, and GA7) in long whips, with GA4 and GA7 found exclusively in long whips and stems. Among the prominent genera present within long whips, Fusarium was solely positively correlated with these gibberellin (GA) hormones, with the exception of GA8, which was positively correlated with Sporisorium. KEGG enrichment analysis linked these hormones to pathways like diterpenoid biosynthesis and plant hormone signal transduction. These findings suggest that Fusarium may influence GA production leading to whip elongation. Our study reveals fungal dynamics and gibberellin responses in sugarcane smut whips. Future research will explore the related molecular gibberellin synthesis mechanisms.},
}
@article {pmid39201270,
year = {2024},
author = {Su, H and Yang, S and Chen, S and Chen, X and Guo, M and Zhu, L and Xu, W and Liu, H},
title = {What Happens in the Gut during the Formation of Neonatal Jaundice-Underhand Manipulation of Gut Microbiota?.},
journal = {International journal of molecular sciences},
volume = {25},
number = {16},
pages = {},
pmid = {39201270},
issn = {1422-0067},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Jaundice, Neonatal/therapy/microbiology/etiology ; Infant, Newborn ; *Probiotics ; *Bilirubin/metabolism/blood ; Breast Feeding ; Milk, Human/microbiology/metabolism ; },
abstract = {Jaundice is a symptom of high blood bilirubin levels affecting about 80% of neonates. In neonates fed with breast milk, jaundice is particularly prevalent and severe, which is likely multifactorial. With the development of genomics and metagenomics, a deeper understanding of the neonatal gut microbiota has been achieved. We find there are accumulating evidence to indicate the importance of the gut microbiota in the mechanism of jaundice. In this paper, we present new comprehensive insight into the relationship between the microbiota and jaundice. In the new perspective, the gut is a crucial crossroad of bilirubin excretion, and bacteria colonizing the gut could play different roles in the excretion of bilirubin, including Escherichia coli as the main traffic jam causers, some Clostridium and Bacteroides strains as the traffic police, and most probiotic Bifidobacterium and Lactobacillus strains as bystanders with no effect or only a secondary indirect effect on the metabolism of bilirubin. This insight could explain why breast milk jaundice causes a longer duration of blood bilirubin and why most probiotics have limited effects on neonatal jaundice. With the encouragement of breastmilk feeding, our perspective could guide the development of new therapy methods to prevent this side effect of breastfeeding.},
}
@article {pmid39201260,
year = {2024},
author = {Ryu, HM and Islam, SMS and Riaz, B and Sayeed, HM and Choi, B and Sohn, S},
title = {Immunomodulatory Effects of a Probiotic Mixture: Alleviating Colitis in a Mouse Model through Modulation of Cell Activation Markers and the Gut Microbiota.},
journal = {International journal of molecular sciences},
volume = {25},
number = {16},
pages = {},
pmid = {39201260},
issn = {1422-0067},
mesh = {Animals ; *Probiotics/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Disease Models, Animal ; *Colitis/microbiology/therapy/diet therapy/chemically induced ; *Dextran Sulfate/toxicity ; RNA, Ribosomal, 16S/genetics ; Colitis, Ulcerative/microbiology/therapy/immunology/diet therapy ; Biomarkers ; Mice, Inbred C57BL ; Colon/microbiology/pathology/metabolism ; },
abstract = {Ulcerative colitis (UC) is a persistent inflammatory intestinal disease that consistently affects the colon and rectum. Its exact cause remains unknown. UC causes a considerable challenge in healthcare, prompting research for novel therapeutic strategies. Although probiotics have gained popularity as possible candidates for managing UC, studies are still ongoing to identify the best probiotics or probiotic mixtures for clinical applications. This study aimed to determine the efficacy of a multi-strain probiotic mixture in mitigating intestinal inflammation in a colitis mouse model induced by dextran sulfate sodium. Specifically, a multi-strain probiotic mixture consisting of Tetragenococcus halophilus and Eubacterium rectale was used to study its impact on colitis symptoms. Anti-inflammatory effects were evaluated using ELISA and flow cytometry. The configuration of gut microbial communities was determined using 16S rRNA metagenomic analysis. According to this study, colitis mice treated with the probiotic mixture experienced reduced weight loss and significantly less colonic shortening compared to untreated mice. Additionally, the treated mice exhibited increased levels of forkhead box P3 (Foxp3) and interleukin 10, along with decreased expression of dendritic cell activation markers, such as CD40+, CD80+, and CD83+, in peripheral blood leukocytes and intraepithelial lymphocytes. Furthermore, there was a significant decrease in the frequencies of CD8+N.K1.1+ cells and CD11b+Ly6G+ cells. In terms of the gut microbiota, probiotic-mixture treatment of colitis mice significantly increased the abundance of the phyla Actinobacteria and Verrucomicrobia (p < 0.05). These results provide valuable insights into the therapeutic promise of multi-strain probiotics, shedding light on their potential to alleviate colitis symptoms. This research contributes to the ongoing exploration of effective probiotic interventions for managing inflammatory bowel disease.},
}
@article {pmid39201258,
year = {2024},
author = {Al-Sarraj, F and Albiheyri, R and Qari, M and Alotaibi, M and Al-Zahrani, M and Anwar, Y and Alghamdi, MA and Nass, NM and Bouback, T and Alotibi, I and Radhwi, O and Sajer, BH and Redhwan, A and Al-Matary, MA and Almanzalawi, EA and Elshafie, HS},
title = {Genetic Patterns of Oral Cavity Microbiome in Patients with Sickle Cell Disease.},
journal = {International journal of molecular sciences},
volume = {25},
number = {16},
pages = {},
pmid = {39201258},
issn = {1422-0067},
support = {grant no. J: 007-130-1443.//Deanship of Scientific Research (DSR) at King Abdulaziz University (KAU), Jeddah/ ; },
mesh = {Humans ; *Anemia, Sickle Cell/microbiology/genetics ; *Mouth/microbiology ; *Microbiota/genetics ; *RNA, Ribosomal, 16S/genetics ; Female ; Male ; Adult ; *Saliva/microbiology ; Bacteria/genetics/classification/isolation &amp; purification ; Young Adult ; Case-Control Studies ; Adolescent ; High-Throughput Nucleotide Sequencing ; Middle Aged ; },
abstract = {The Middle Eastern prevalence of sickle cell anemia, a genetic disorder that affects red blood cells, necessitates additional research. On a molecular level, we sought to identify and sort the oral microbiota of healthy individuals and those with sickle cell anemia. Furthermore, it is crucial to comprehend how changes in the genetic makeup of the oral microbiota impact the state of sickle cell anemia. Using next-generation sequencing, the 16S rRNA amplicon was examined using saliva samples from 36 individuals with sickle cell anemia and healthy individuals. These samples were obtained from sickle cell anemia patients (18 samples) and healthy control participants (controls, 18 samples). Various analyses are conducted using bioinformatic techniques to identify distinct species and their relative abundance. Streptococcus, followed by Fusobacterium nucleatum, Prevotella, and Veillonella were the most prevalent genera of bacteria in the saliva of the SCA and non-SCA individuals according to our findings. Rothia mucilaginosa, Prevotella scoposa, and Veillonella dispar species were the dominant species in both sickle cell anemia and non-sickle cell anemia subjects. Streptococcus salivarius, Actinomyces graevenitzii, Actinomyces odontolyticus, and Actinomyces georgiae spp. were the most prevalent bacterial spp. in the studied SCA cases. The sequencing of the 16S rRNA gene yielded relative abundance values that were visualized through a heatmap analysis. Alterations in the oral microflora's constitution can significantly affect the susceptibility of sickle cell anemia patients to develop more severe health complications. Salivary diagnosis is a potential tool for predicting and preventing oral microbiome-related diseases in the future.},
}
@article {pmid39200000,
year = {2024},
author = {Lowe, M and Strasheim, W and Chan, WY and Perovic, O},
title = {Bacterial and Genetic Features of Raw Retail Pork Meat: Integrative Analysis of Antibiotic Susceptibility, Whole-Genome Sequencing, and Metagenomics.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {8},
pages = {},
pmid = {39200000},
issn = {2079-6382},
support = {D43 TW011255/TW/FIC NIH HHS/United States ; GRANT AE89 (ANTIMICROBIAL RESISTANCE PREVALENCE AND TRANSMISSION BETWEEN ANIMAL FEED AND HUMANS)//South African Medical Research Council/ ; },
abstract = {The global antibiotic resistance crisis, driven by overuse and misuse of antibiotics, is multifaceted. This study aimed to assess the microbiological and genetic characteristics of raw retail pork meat through various methods, including the isolation, antibiotic susceptibility testing (AST), whole-genome sequencing (WGS) of selected indicator bacteria, antibiotic residue testing, and metagenomic sequencing. Samples were purchased from 10 pre-selected retail stores in Gauteng, South Africa. The samples were aseptically separated, with portions sent to an external laboratory for isolating indicator bacteria and testing for antibiotic residues. Identification of the isolated bacteria was reconfirmed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). AST was performed using the Microscan Walkaway system (Beckman Coulter, Brea, CA, USA). WGS and metagenomic sequencing were performed using the Illumina NextSeq 550 instrument (San Diego, CA, USA). The isolated E. coli and E. faecalis exhibited minimal phenotypic resistance, with WGS revealing the presence of tetracycline resistance genes. Both the isolated bacteria and meat samples harboured tetracycline resistance genes and the antibiotic residue concentrations were within acceptable limits for human consumption. In the metagenomic context, most identified bacteria were of food/meat spoilage and environmental origin. The resistome analysis primarily indicated beta-lactam, tetracycline and multidrug resistance genes. Further research is needed to understand the broader implications of these findings on environmental health and antibiotic resistance.},
}
@article {pmid39199499,
year = {2024},
author = {Mabrok, HB and Ramadan, AA and Hamed, IM and Mohamed, DA},
title = {Obesity as Inducer of Cognitive Function Decline via Dysbiosis of Gut Microbiota in Rats.},
journal = {Brain sciences},
volume = {14},
number = {8},
pages = {},
pmid = {39199499},
issn = {2076-3425},
support = {a626035bfd925943, 4c6c6a0dc9645904, 175e6bf937114ef5, 18dca4e8f29e587c, aaf09103eb8bd6ee, 3740a1d4a23d772f, 1b07773fd3c8c954, 4f8fa1a570a3a4b7, 490e7e4e51713e71, 1e87a07edec11a96, 7642f29d62c1068b, c06bc3bf279a8491, c78b30a55528e880, e160d996ffb69ed4, 133//Discount Vouchers/ ; },
abstract = {Diet-induced obesity is a global phenomenon that affects the population worldwide with manifestations at both the phenotypic and genotypic levels. Cognitive function decline is a major global health challenge. The relation between obesity and cognitive function is a debatable issue. The main goal of the current research was to study the implications of obesity on cognitive function and gut microbiota diversity and its impact on plasma and brain metabolic parameters in rats. Obesity was induced in rats by feeding on a high-fat (HF) or a high-fat/high-sucrose (HFHS) diet. The results reveal that both the HF (0.683) and HFHS (0.688) diets were effective as obesity inducers, which was confirmed by a significant increase in the body mass index (BMI). Both diet groups showed dyslipidemia and elevation of oxidative stress, insulin resistance (IR), and inflammatory markers with alterations in liver and kidney functions. Obesity led to a reduction in cognitive function through a reduction in short-term memory by 23.8% and 30.7% in the rats fed HF and HFHS diets, respectively, and learning capacity and visuo-spatial memory reduced by 8.9 and 9.7 s in the rats fed an HF or HFHS diet, respectively. Bacteroidetes, Firmicutes, Proteobacteria, Fusobacteria, and Spirochaetes phyla were detected. The Firmicutes/Bacteroidetes ratio (F/B) significantly decreased in the HF group, while it increased in the HFHS group compared to the normal control. The two species, Bacteroides acidifaciens and Bacteroides ovatus, which are associated with IR, were drastically compromised by the high-fat/high-sucrose diet. Some species that have been linked to reduced inflammation showed a sharp decrease in the HFHS group, while Prevotella copri, which is linked to carbohydrate metabolism, was highly enriched. In conclusion: Obesity led to cognitive impairment through changes in short-term and visuo-spatial memory. A metagenomic analysis revealed alterations in the abundance of some microbial taxa associated with obesity, inflammation, and insulin resistance in the HF and HFHS groups.},
}
@article {pmid39198891,
year = {2024},
author = {Tian, F and Wainaina, JM and Howard-Varona, C and Domínguez-Huerta, G and Bolduc, B and Gazitúa, MC and Smith, G and Gittrich, MR and Zablocki, O and Cronin, DR and Eveillard, D and Hallam, SJ and Sullivan, MB},
title = {Prokaryotic-virus-encoded auxiliary metabolic genes throughout the global oceans.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {159},
pmid = {39198891},
issn = {2049-2618},
support = {ABI#1759874, ABI#2149505, OCE#1536989, OCE#1829831, and OCE#2019589//National Science Foundation/ ; #3790//Gordon and Betty Moore Foundation Investigator Award/ ; },
mesh = {*Oceans and Seas ; *Seawater/virology/microbiology ; Metagenomics ; Bacteria/genetics/classification/metabolism ; Viruses/genetics/classification/isolation &amp; purification ; Prokaryotic Cells/metabolism/virology ; Metagenome ; Metabolic Networks and Pathways/genetics ; Gene Transfer, Horizontal ; Phosphatidylethanolamines/metabolism ; },
abstract = {BACKGROUND: Prokaryotic microbes have impacted marine biogeochemical cycles for billions of years. Viruses also impact these cycles, through lysis, horizontal gene transfer, and encoding and expressing genes that contribute to metabolic reprogramming of prokaryotic cells. While this impact is difficult to quantify in nature, we hypothesized that it can be examined by surveying virus-encoded auxiliary metabolic genes (AMGs) and assessing their ecological context.<br><br>RESULTS: We systematically developed a global ocean AMG catalog by integrating previously described and newly identified AMGs and then placed this catalog into ecological and metabolic contexts relevant to ocean biogeochemistry. From 7.6 terabases of Tara Oceans paired prokaryote- and virus-enriched metagenomic sequence data, we increased known ocean virus populations to 579,904 (up 16%). From these virus populations, we then conservatively identified 86,913 AMGs that grouped into 22,779 sequence-based gene clusters, 7248 (~&#x2009;32%) of which were not previously reported. Using our catalog and modeled data from mock communities, we estimate that&#x2009;~&#x2009;19% of ocean virus populations carry at least one AMG. To understand AMGs in their metabolic context, we identified 340 metabolic pathways encoded by ocean microbes and showed that AMGs map to 128 of them. Furthermore, we identified metabolic "hot spots" targeted by virus AMGs, including nine pathways where most steps (&#x2265;&#x2009;0.75) were AMG-targeted (involved in carbohydrate, amino acid, fatty acid, and nucleotide metabolism), as well as other pathways where virus-encoded AMGs outnumbered cellular homologs (involved in lipid A phosphates, phosphatidylethanolamine, creatine biosynthesis, phosphoribosylamine-glycine ligase, and carbamoyl-phosphate synthase pathways).<br><br>CONCLUSIONS: Together, this systematically curated, global ocean AMG catalog and analyses provide a valuable resource and foundational observations to understand the role of viruses in modulating global ocean metabolisms and their biogeochemical implications. Video Abstract.},
}
@article {pmid39198832,
year = {2024},
author = {Su, W and Gong, C and Zhong, H and Yang, H and Chen, Y and Wu, X and Jin, J and Xi, H and Zhao, J},
title = {Vaginal and endometrial microbiome dysbiosis associated with adverse embryo transfer outcomes.},
journal = {Reproductive biology and endocrinology : RB&amp;E},
volume = {22},
number = {1},
pages = {111},
pmid = {39198832},
issn = {1477-7827},
support = {437606312//Wenzhou Medical University advantageous and distinctive Discipline Construction Project/ ; },
mesh = {Humans ; Female ; *Embryo Transfer/methods ; *Dysbiosis/microbiology ; Adult ; *Vagina/microbiology ; *Microbiota/genetics/physiology ; *Endometrium/microbiology/metabolism ; *Embryo Implantation/physiology ; Pregnancy ; *Infertility, Female/microbiology/therapy ; Fertilization in Vitro/methods ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: Assisted reproductive technology (ART) is the most effective method to treat infertility and the pathogenesis of implantation failure after in vitro fertilization-embryo transfer (IVF-ET) is a challenging filed in infertility. Microbes in the female reproductive tract are considered to be associated with gynecological and obstetric diseases. However, its effects on embryo implantation failure are unsured.<br><br>PURPOSE: This study aimed to investigate reproductive tract dysbiosis, identify different bacteria in reproductive tract as potential biomarkers of embryo implantation failure and demonstrate the pathogenesis through metabolites analysis.<br><br>METHODS: We compared the data from 16S rRNA gene and metagenome in reproductive tracts through QIIME2 and HUMAnN2 by the times of embryo implantation failure on 239 infertile patients and 17 healthy women.<br><br>RESULTS: Our study revealed a strong positive correlation between Lactobacillus abundance and embryo implantation success (IS) after IVF-ET. The microbial community composition and structure in reproductive tract showed substantially difference between the embryo implantation failure (IF) and healthy control. Moreover, we established a diagnostic model through receiver operating characteristic (ROC) with 0.913 area under curve (AUC) in IS and multiple implantation failures (MIF), verified its effectiveness with an AUC&#x2009;=&#x2009;0.784 demonstrating microbial community alterations could efficiently discriminate MIF patients. Metagenome functional analyses of vaginal samples from another independent infertile patients after IVF-ET revealed the L-lysine synthesis pathway enriched in IF patients, along with ascended vaginal pH and decreased Lactobacillus abundance.<br><br>CONCLUSIONS: This study clarifies several independent relationships of bacteria in vagina and endometrial fluid on embryo implantation failure and undoubtedly broadens the understanding about female reproductive health.},
}
@article {pmid39198826,
year = {2024},
author = {Su, Q and Zhuang, DH and Li, YC and Chen, Y and Wang, XY and Ge, MX and Xue, TY and Zhang, QY and Liu, XY and Yin, FQ and Han, YM and Gao, ZL and Zhao, L and Li, YX and Lv, MJ and Yang, LQ and Xia, TR and Luo, YJ and Zhang, Z and Kong, QP},
title = {Gut microbiota contributes to high-altitude hypoxia acclimatization of human populations.},
journal = {Genome biology},
volume = {25},
number = {1},
pages = {232},
pmid = {39198826},
issn = {1474-760X},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Acclimatization ; *Altitude ; Animals ; Adult ; Male ; *Hypoxia/genetics ; Mice ; Female ; Longitudinal Studies ; Altitude Sickness/microbiology/genetics ; Middle Aged ; },
abstract = {BACKGROUND: The relationship between human gut microbiota and high-altitude hypoxia acclimatization remains highly controversial. This stems primarily from uncertainties regarding both the potential temporal changes in the microbiota under such conditions and the existence of any dominant or core bacteria that may assist in host acclimatization.<br><br>RESULTS: To address these issues, and to control for variables commonly present in previous studies which significantly impact the results obtained, namely genetic background, ethnicity, lifestyle, and diet, we conducted a 108-day longitudinal study on the same cohort comprising 45 healthy Han adults who traveled from lowland Chongqing, 243 masl, to high-altitude plateau Lhasa, Xizang, 3658 masl, and back. Using shotgun metagenomic profiling, we study temporal changes in gut microbiota composition at different timepoints. The results show a significant reduction in the species and functional diversity of the gut microbiota, along with a marked increase in functional redundancy. These changes are primarily driven by the overgrowth of Blautia A, a genus that is also abundant in six independent Han cohorts with long-term duration in lower hypoxia environment in Shigatse, Xizang, at 4700 masl. Further animal experiments indicate that Blautia A-fed mice exhibit enhanced intestinal health and a better acclimatization phenotype to sustained hypoxic stress.<br><br>CONCLUSIONS: Our study underscores the importance of Blautia A species in the gut microbiota's rapid response to high-altitude hypoxia and its potential role in maintaining intestinal health and aiding host adaptation to extreme environments, likely via anti-inflammation and intestinal barrier protection.},
}
@article {pmid39198450,
year = {2024},
author = {Licht, P and Dominelli, N and Kleemann, J and Pastore, S and Müller, ES and Haist, M and Hartmann, KS and Stege, H and Bros, M and Meissner, M and Grabbe, S and Heermann, R and Mailänder, V},
title = {The skin microbiome stratifies patients with cutaneous T cell lymphoma and determines event-free survival.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {74},
pmid = {39198450},
issn = {2055-5008},
mesh = {Humans ; *Microbiota ; *Skin/microbiology ; Female ; Middle Aged ; Male ; *Staphylococcus aureus/genetics/pathogenicity/isolation &amp; purification ; *Lymphoma, T-Cell, Cutaneous/microbiology ; Aged ; *Mycosis Fungoides/microbiology ; Dysbiosis/microbiology ; Skin Neoplasms/microbiology/pathology ; Adult ; Aged, 80 and over ; Metagenomics/methods ; Virulence Factors/genetics ; Bacteria/classification/genetics/isolation &amp; purification ; },
abstract = {Mycosis fungoides (MF) is the most common entity of Cutaneous T cell lymphomas (CTCL) and is characterized by the presence of clonal malignant T cells in the skin. The role of the skin microbiome for MF development and progression are currently poorly understood. Using shotgun metagenomic profiling, real-time qPCR, and T cell receptor sequencing, we compared lesional and nonlesional skin of 20 MF patients with early and advanced MF. Additionally, we isolated Staphylococcus aureus and other bacteria from MF skin for functional profiling and to study the S. aureus virulence factor spa. We identified a subgroup of MF patients with substantial dysbiosis on MF lesions and concomitant outgrowth of S. aureus on plaque-staged lesions, while the other MF patients had a balanced microbiome on lesional skin. Dysbiosis and S. aureus outgrowth were accompanied by ectopic levels of cutaneous antimicrobial peptides (AMPs), including adaptation of the plaque-derived S. aureus strain. Furthermore, the plaque-derived S. aureus strain showed a reduced susceptibility towards antibiotics and an upregulation of the virulence factor spa, which may activate the NF-κB pathway. Remarkably, patients with dysbiosis on MF lesions had a restricted T cell receptor repertoire and significantly lower event-free survival. Our study highlights the potential for microbiome-modulating treatments targeting S. aureus to prevent MF progression.},
}
@article {pmid39198444,
year = {2024},
author = {Chang, D and Gupta, VK and Hur, B and Cobo-López, S and Cunningham, KY and Han, NS and Lee, I and Kronzer, VL and Teigen, LM and Karnatovskaia, LV and Longbrake, EE and Davis, JM and Nelson, H and Sung, J},
title = {Gut Microbiome Wellness Index 2 enhances health status prediction from gut microbiome taxonomic profiles.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {7447},
pmid = {39198444},
issn = {2041-1723},
support = {UL1 TR002377/TR/NCATS NIH HHS/United States ; UL1 TR002494/TR/NCATS NIH HHS/United States ; UL1TR002377//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; },
mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; *Feces/microbiology ; *Health Status ; Metagenome ; Bacteria/classification/genetics/isolation &amp; purification ; Female ; },
abstract = {Recent advancements in translational gut microbiome research have revealed its crucial role in shaping predictive healthcare applications. Herein, we introduce the Gut Microbiome Wellness Index 2 (GMWI2), an enhanced version of our original GMWI prototype, designed as a standardized disease-agnostic health status indicator based on gut microbiome taxonomic profiles. Our analysis involves pooling existing 8069 stool shotgun metagenomes from 54 published studies across a global demographic landscape (spanning 26 countries and six continents) to identify gut taxonomic signals linked to disease presence or absence. GMWI2 achieves a cross-validation balanced accuracy of 80% in distinguishing healthy (no disease) from non-healthy (diseased) individuals and surpasses 90% accuracy for samples with higher confidence (i.e., outside the "reject option"). This performance exceeds that of the original GMWI model and traditional species-level α-diversity indices, indicating a more robust gut microbiome signature for differentiating between healthy and non-healthy phenotypes across multiple diseases. When assessed through inter-study validation and external validation cohorts, GMWI2 maintains an average accuracy of nearly 75%. Furthermore, by reevaluating previously published datasets, GMWI2 offers new insights into the effects of diet, antibiotic exposure, and fecal microbiota transplantation on gut health. Available as an open-source command-line tool, GMWI2 represents a timely, pivotal resource for evaluating health using an individual's unique gut microbial composition.},
}
@article {pmid39198442,
year = {2024},
author = {Campos-Madueno, EI and Aldeia, C and Endimiani, A},
title = {Nanopore R10.4 metagenomic detection of blaCTX-M/blaDHA antimicrobial resistance genes and their genetic environments in stool.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {7450},
pmid = {39198442},
issn = {2041-1723},
support = {192514//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; },
mesh = {*Feces/microbiology ; *Escherichia coli/genetics/isolation &amp; purification ; Humans ; *beta-Lactamases/genetics/metabolism ; *Metagenomics/methods ; *Nanopores ; Escherichia coli Proteins/genetics ; Plasmids/genetics ; Nanopore Sequencing/methods ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Gastrointestinal Microbiome/genetics ; },
abstract = {The increasing prevalence of gut colonization with CTX-M extended-spectrum β-lactamase- and/or DHA plasmid-mediated AmpC-producing Escherichia coli is a concern. Here, we evaluate Nanopore-shotgun metagenomic sequencing (Nanopore-SMS) latest V14 chemistry to detect blaCTX-M and blaDHA genes from healthy stools. We test 25 paired samples characterized with culture-based methods (native and pre-enriched). Antimicrobial resistant genes (ARGs) are detected from reads and meta-assembled genomes (MAGs) to determine their associated genetic environments (AGEs). Sensitivity and specificity of native Nanopore-SMS are 61.1% and 100%, compared to 81.5% and 75% for pre-enriched Nanopore-SMS, respectively. Native Nanopore-SMS identifies only one sample with an AGE, whereas pre-enriched Nanopore-SMS recognizes 9/18 plasmids and 5/9 E. coli chromosomes. Pre-enriched Nanopore-SMS identifies more ARGs than native Nanopore-SMS (p < 0.001). Notably, blaCTX-Ms and blaDHAs AGEs (plasmid and chromosomes) are identified within 1 hour of sequencing. Furthermore, microbiota analyses show that pre-enriched Nanopore-SMS results in more E. coli classified reads (47% vs. 3.1%), higher differential abundance (5.69 log2 fold) and lower Shannon diversity index (p < 0.0001). Nanopore-SMS has the potential to be used for intestinal colonization screening. However, sample pre-enrichment is necessary to increase sensitivity. Further computational improvements are needed to reduce the turnaround time for clinical applications.},
}
@article {pmid39198293,
year = {2024},
author = {Joseph, B and Babu, S},
title = {Effect of Organic and Chemical Fertilizer on the Diversity of Rhizosphere and Leaf Microbial Composition in Sunflower Plant.},
journal = {Current microbiology},
volume = {81},
number = {10},
pages = {331},
pmid = {39198293},
issn = {1432-0991},
mesh = {*Fertilizers/analysis ; *Rhizosphere ; *Helianthus/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification/drug effects ; *Plant Leaves/microbiology ; *Soil Microbiology ; *Fungi/classification/genetics/isolation &amp; purification ; *Manure/microbiology ; Microbiota ; Biodiversity ; Metagenomics ; },
abstract = {Applying organic manure to crops positively impacts the soil microbial community which is negatively impacted when chemical fertilizers are used. Organic manures also add new microbes to the soil in addition to influencing the growth of native ones. Metagenomic analysis of different organic manures, soil, and pot culture experiments conducted under various fertilizer conditions constitute the primary methodologies employed in this study. We compared the effect of two organic manure combinations and an inorganic fertilizer combination on microbial community of rhizosphere soil and leaves of sunflower plants. Metagenomic sequencing data analysis revealed that the diversity of bacteria and fungi is higher in organic manure than in chemical fertilizers. Each organic manure combination selectively increased population of some specific microbes and supported new microbes. Application of chemical fertilizer hurts many plant beneficial fungi and bacteria. In summary, our study points out the superiority of organic manure combinations in enhancing microbial diversity and supporting beneficial microbes. These findings enhance the profound influence of fertilizer types on sunflower microbial communities, shedding light on the intricate dynamics within the rhizosphere and leaf microbiome. Bacterial genera such as Bacillus, Serratia, Sphingomonas, Pseudomonas, Methylobacterium, Acinetobacter, Stenotrophomonas, and fungal genera such as Wallemia, Aspergillus, Cladosporium, and Penicillium constitute the key microbes of sunflower plants.},
}
@article {pmid39197657,
year = {2024},
author = {Khan, AS and Afrin, S and Ahmed, F and Rahman, SR},
title = {Shotgun metagenomic analysis reveals the emergence of plasmid-encoded mcr-5.1 gene in hospital wastewater in Bangladesh.},
journal = {Journal of global antimicrobial resistance},
volume = {39},
number = {},
pages = {22-26},
doi = {10.1016/j.jgar.2024.08.007},
pmid = {39197657},
issn = {2213-7173},
abstract = {Colistin is considered the last line therapy for treating multidrug-resistant (MDR) bacterial infections in humans. Therefore, the spread of colistin resistance poses a serious threat to human, and environmental health. Though Bangladesh is known as a hotspot of AMR, limited studies have been carried out regarding the status of colistin resistance. Information on the emerging bacterial resistance is inevitable for protecting public health. Nowadays, wastewater analysis has been prioritized for metagenomics-enabled AMR surveillance. Our study on the metagenomic analysis of untreated hospital effluents first detected the colistin resistance-conferring mcr-5.1 gene in the hospital environment of Bangladesh. Phylogenetic tree and in silico AMR analysis confirmed the detection of this mcr-5 variant, which is located in a plasmid contig. The plasmid was untypeable and belonged to the bacteria from the Enterobacteriaceae family. The mcr-5.1 operon was embedded in a Tn3 transposon, suggesting the mobility of the gene. Tnshfr1 transposon, chromate resistance protein ChrB, DNA invertase hin, and two MFS-type proteins were present in the genetic environment of mcr-5.1. Our findings provide evidence of the occurrence of mcr-5.1 in a hospital environment in Bangladesh, which calls for immediate attention and effective measures to contain the dissemination of colistin resistance in the environment.},
}
@article {pmid39197649,
year = {2024},
author = {Pinel-Cabello, M and Wasmund, K and Soder-Walz, JM and Vega, M and Rosell, M and Marco-Urrea, E},
title = {Divergent dual C-H isotopic fractionation pattern during anaerobic biodegradation of toluene within Aromatoleum species under nitrate-reducing conditions.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {361},
number = {},
pages = {124823},
doi = {10.1016/j.envpol.2024.124823},
pmid = {39197649},
issn = {1873-6424},
abstract = {Toluene is a pollutant frequently detected in contaminated groundwater, mostly due to leakage from underground gasoline storage tanks and pipeline ruptures. Multi-element compound-specific isotope analysis provides a framework to understand transformation processes and design efficient remediation strategies. In this study, we enriched an anaerobic bacterial culture derived from a BTEX-contaminated aquifer that couples toluene and phenol oxidation with nitrate reduction and the concomitant production of carbon dioxide and biomass. The 16S rRNA gene amplicon data indicated that the toluene-degrading consortium was dominated by an Aromatoleum population (87 ± 2 % relative abundance), and metagenome sequencing confirmed that the genome of this Aromatoleum sp. encoded glycyl-radical enzyme benzylsuccinate synthase (BssABC) and phenylphospate synthase (PpsA1BC) homologous genes involved in the first step of toluene and phenol transformation, respectively. Carbon and hydrogen isotopic fractionation were εbulk, C = - 3.5 ± 0.6 ‰ and εrp, H = - 85 ± 11 ‰, respectively, leading to a dual C-H isotope slope of Λ[H/C] = 26 ± 2. This value fits with a previously reported value for a consortium dominated by an Azoarcus species (Λ[H/C] = 19 ± 5) but differs from that reported for Aromatoleum aromaticum (Λ[H/C] = 14 ± 1), both of which grow with toluene under nitrate-reducing conditions. Overall, this suggests the existence of different BssABC enzymes with different mechanistic motifs even within the same Aromatoleum genus.},
}
@article {pmid39197646,
year = {2024},
author = {Yang, T and Zhou, X and Wu, Y and Liang, Y and Zeng, X and Yu, Z},
title = {Metagenomic analyses of aerobic bacterial enrichment cultures that degraded Tris(2-chloroethyl) phosphate (TCEP) and its transformation products.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {361},
number = {},
pages = {124825},
doi = {10.1016/j.envpol.2024.124825},
pmid = {39197646},
issn = {1873-6424},
abstract = {Tris(2-chloroethyl) phosphate (TCEP) is of growing public concern worldwide because of its ubiquitous contamination, toxicity, and persistence. In this study, we investigated bacterial communities in aerobic enrichment cultures with TCEP and its two major transformation products bis(2-chloroethyl) phosphate (BCEP) and 2-chloroethanol (2-CE) as the sole carbon source. Burkholderiales and Rhizobiales were likely two main bacterial guilds involved in the hydrolysis of TCEP, while Rhizobiales and Sphingomonadales may play an important role in the hydrolysis of BCEP, given the increase of Rhizobiales and Sphingomonadales-related phosphoesterase genes when the carbon source was switched from TCEP to BCEP. All Burkholderiales, Rhizobiales, Sphingomonadales were probably efficient in 2-CE metabolism, because their dehydrogenase genes and dehalogenase genes increased after 2-CE enrichment. The different substrate preference of different bacterial guilds highlighted the importance to understand the diversity and collaboration among functional bacteria. Meanwhile, two TCEP-degrading strains affiliated with Xanthobacter and Ancylobacter were isolated. Xanthobacter sp. strain T2-1 was able to degrade both TCEP and BCEP following the pseudo-first-order kinetics with reaction rates of 1.66 h[-1] for TCEP and 1.02 h[-1] for BCEP, respectively. Ancylobacter sp. strain T3-4 could degrade TCEP following the pseudo-first-order kinetics with a reaction rate of 2.54 h[-1], but is unable to degrade BCEP. Additionally, strains that were phylogenetically closely related were found to have different degradation capabilities toward TCEP and/or BCEP, indicating the importance to investigate functional genes such as phosphoesterase genes.},
}
@article {pmid39197642,
year = {2024},
author = {Ning, Z and Sheng, Y and Gan, S and Guo, C and Wang, S and Cai, P and Zhang, M},
title = {Metagenomic and isotopic insights into carbon fixation by autotrophic microorganisms in a petroleum hydrocarbon impacted red clay aquifer.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {361},
number = {},
pages = {124824},
doi = {10.1016/j.envpol.2024.124824},
pmid = {39197642},
issn = {1873-6424},
abstract = {Autotrophic microorganisms, the pivotal carbon fixers, exhibit a broad distribution across diverse environments, playing critical roles in the process of carbon sequestration. However, insights into their distribution characteristics in aquifers, particularly in those petroleum-hydrocarbon-contaminated (PHC) aquifers that were known for rich in heterotrophs, have been limited. In the study, groundwater samples were collected from red clay aquifers in the storage tank leakage area of a PHC site, a prevalent aquifer type in southern China and other regions. Metagenomics combined with hydrochemical and inorganic carbon isotope analyses were employed to elucidate the presence of microbial carbon fixation and its driving forces. Results showed that there were hundreds of autotrophic microorganisms participating in distinct carbon fixation processes in the red clay PHC aquifers. Reductive tricarboxylic acid (rTCA) and dicarboxylate/4-hydroxybutyrate (DC/4HB), as well as 3-hydroxypropionate (3HP or/and 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB)) were the predominant carbon fixation pathways. The abundances of carbon fixation genes and autotrophic microorganisms were significantly and positively correlated with hydrocarbon concentrations and δ[13]C of dissolved inorganic carbon (δ[13]C-DIC) values. This finding indicated that the petroleum hydrocarbon significantly promoted the proliferation of carbon fixation microorganisms, leading to a substantial uptake of inorganic carbon. Therefore, we deduce that this process holds considerable potential for carbon sequestration in PHC-contaminated aquifers.},
}
@article {pmid39197546,
year = {2024},
author = {Kim, H and Lee, E and Park, M and Min, K and Diep, YN and Kim, J and Ahn, H and Lee, E and Kim, S and Kim, Y and Kang, YJ and Jung, JH and Byun, MS and Joo, Y and Jeong, C and Lee, DY and Cho, H and Park, H and Kim, T},
title = {Microbiome-derived indole-3-lactic acid reduces amyloidopathy through aryl-hydrocarbon receptor activation.},
journal = {Brain, behavior, and immunity},
volume = {122},
number = {},
pages = {568-582},
doi = {10.1016/j.bbi.2024.08.051},
pmid = {39197546},
issn = {1090-2139},
mesh = {Animals ; Female ; Humans ; Male ; Mice ; *Alzheimer Disease/metabolism ; *Amyloid beta-Peptides/metabolism ; Amyloidosis/metabolism ; Astrocytes/metabolism ; Brain/metabolism ; Cognitive Dysfunction/metabolism ; *Disease Models, Animal ; *Gastrointestinal Microbiome/drug effects ; *Indoles/pharmacology ; Mice, Transgenic ; Microbiota/drug effects ; Microglia/metabolism ; *Receptors, Aryl Hydrocarbon/metabolism ; Signal Transduction/drug effects ; Tryptophan/metabolism/pharmacology ; },
abstract = {Alzheimer's disease (AD) pathogenesis has been associated with the gut microbiome and its metabolites, though the specific mechanisms have remained unclear. In our study, we used a multi-omics approach to identify specific microbial strains and metabolites that could potentially mitigate amyloidopathy in 5xFAD mice, a widely used model for AD research. Among the microbial strains tested, three showed promising results in reducing soluble amyloid-beta (Aβ) levels. Plasma metabolomics analysis revealed an enrichment of tryptophan (Trp) and indole-3-lactic acid (ILA) in mice with reduced soluble Aβ levels, suggesting a potential preventative role. The administration of a combined treatment of Trp and ILA prevented both Aβ accumulation and cognitive impairment in the 5xFAD mice. Our investigation into the mechanism revealed that ILA's effect on reducing Aβ levels was mediated through the activation of microglia and astrocytes, facilitated by the aryl hydrocarbon receptor (AhR) signaling pathway. These mechanisms were verified through experiments in 5xFAD mice that included an additional group with the administration of ILA alone, as well as in vitro experiments using an AhR inhibitor. Clinical data analysis revealed a greater abundance of Lactobacillus reuteri in the gut of healthy individuals compared to those at early stages of Aβ accumulation or with mild cognitive impairment. Additionally, human post-mortem brain analyses showed an increased expression of genes associated with the AhR signaling pathway in individuals without AD, suggesting a protective effect against AD progression. Our results indicate that ILA from gut microbes could inhibit the progression of amyloidopathy in 5xFAD mice through activation of AhR signaling in the brain.},
}
@article {pmid39197493,
year = {2024},
author = {Fu, R and Xu, J and Fan, Z and Qu, H and Jiang, Y and Xiong, W and Huang, F and Xuan, L and Xu, N and Liu, H and Wang, Z and Sun, J and Liu, Q and Lin, R},
title = {Metagenomic Next-Generation Sequencing in the Diagnosis of Pulmonary Infections after Allogeneic Hematopoietic Stem Cell Transplantation.},
journal = {Transplantation and cellular therapy},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jtct.2024.08.014},
pmid = {39197493},
issn = {2666-6367},
abstract = {Early and accurate identification of pathogens in pulmonary infections after allogeneic hematopoietic stem cell transplantation (allo-HSCT) is critically important. The clinical usefulness of metagenomic next-generation sequencing (mNGS) in the diagnosis of pulmonary infections after allo-HSCT remains under discussion. This multicenter retrospective study was conducted to compare mNGS and conventional microbiological tests (CMTs) in identifying the pathogens of pulmonary infections in allo-HSCT recipients. One hundred forty allo-HSCT recipients with suspected pulmonary infections who underwent bronchoscopy were included. mNGS and CMTs performed on bronchoalveolar lavage fluid specimens showed 71.4% positivity on mNGS compared to 55.0% positivity on CMTs. mNGS identified 182 pathogens, including bacteria (n = 88), fungi (n = 35) and viruses (n = 59), compared to 106 pathogens detected by CMTs (bacteria, n = 31; fungi, n = 24; viruses, n = 51). Pulmonary infection was finally diagnosed in 98 patients, including 22 bacterial, 7 fungal, 18 viral, and 48 mixed infections and 3 infections with an unknown pathogen. Mixed infections were identified in 50.5% of the patients with pulmonary infection. The sensitivity of mNGS and CMTs for diagnosing pulmonary infections was 88.8% and 69.4%, respectively (P = .001), and the specificity were 81.0% and 85.7%, respectively (P = .688). Our findings suggest that mNGS may be a promising technology for diagnosing pulmonary infections in allo-HSCT recipients.},
}
@article {pmid39197484,
year = {2024},
author = {Lu, W and Zheng, Y and Wang, Y and Song, J and Weng, Y and Ma, W and Arslan, M and Gamal El-Din, M and Wang, D and Wang, Q and Chen, C},
title = {Survival strategies and assembly mechanisms of microbial communities in petroleum-contaminated soils.},
journal = {Environmental research},
volume = {262},
number = {Pt 1},
pages = {119857},
doi = {10.1016/j.envres.2024.119857},
pmid = {39197484},
issn = {1096-0953},
abstract = {This study analyzed petroleum-contaminated soils from south and north locations in China to explore the structure, diversity, functional genes and assembly processes of microbial communities' . Compared with soils from south locations, soils from northern regions exhibited elevated pH, total nitrogen (TN), and total petroleum hydrocarbon (TPH) levels. Among these, TN and TPH were the most influential on the microbial community. The dominant phyla for bacteria, archaea, and fungi were Proteobacteria, Thaumarchaeota, and Ascomycota, respectively. Among them, Proteobacteria was strongly correlated with various functional genes including alkB and many aromatics degradation and denitrification genes (r > 0.9, p < 0.01), suggesting that Proteobacteria play an important role in petroleum-contaminated soils. Metabolism in northern regions was more active than that in southern regions. The northern regions showed a pronounced tendency for denitrification, while the southern regions were characterized by acetoclastic methanogenesis. The assembly of microbial communities exhibited regional patterns, the deterministic assembly was more prominent in the northern soils, while the stochastic assembly was evident in the southern soils. Overall, these findings provide a new conceptual framework to understand the biosphere in petroleum-contaminated soil, potentially guiding improved management practices in the environmental remediation.},
}
@article {pmid39197454,
year = {2024},
author = {Thänert, R and Schwartz, DJ and Keen, EC and Hall-Moore, C and Wang, B and Shaikh, N and Ning, J and Rouggly-Nickless, LC and Thänert, A and Ferreiro, A and Fishbein, SRS and Sullivan, JE and Radmacher, P and Escobedo, M and Warner, BB and Tarr, PI and Dantas, G},
title = {Clinical sequelae of gut microbiome development and disruption in hospitalized preterm infants.},
journal = {Cell host &amp; microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2024.07.027},
pmid = {39197454},
issn = {1934-6069},
support = {2021081/DDCF/Doris Duke Charitable Foundation/United States ; K08 AI159384/AI/NIAID NIH HHS/United States ; },
abstract = {Aberrant preterm infant gut microbiota assembly predisposes to early-life disorders and persistent health problems. Here, we characterize gut microbiome dynamics over the first 3 months of life in 236 preterm infants hospitalized in three neonatal intensive care units using shotgun metagenomics of 2,512 stools and metatranscriptomics of 1,381 stools. Strain tracking, taxonomic and functional profiling, and comprehensive clinical metadata identify Enterobacteriaceae, enterococci, and staphylococci as primarily exploiting available niches to populate the gut microbiome. Clostridioides difficile lineages persist between individuals in single centers, and Staphylococcus epidermidis lineages persist within and, unexpectedly, between centers. Collectively, antibiotic and non-antibiotic medications influence gut microbiome composition to greater extents than maternal or baseline variables. Finally, we identify a persistent low-diversity gut microbiome in neonates who develop necrotizing enterocolitis after day of life 40. Overall, we comprehensively describe gut microbiome dynamics in response to medical interventions in preterm, hospitalized neonates.},
}
@article {pmid39197279,
year = {2024},
author = {Guo, Y and Cheng, S and Fang, H and Geng, J and Li, Y and Shi, F and Wang, H and Chen, L and Zhou, Y},
title = {Copper and cadmium co-contamination increases the risk of nitrogen loss in red paddy soils.},
journal = {Journal of hazardous materials},
volume = {479},
number = {},
pages = {135626},
doi = {10.1016/j.jhazmat.2024.135626},
pmid = {39197279},
issn = {1873-3336},
mesh = {*Cadmium/toxicity/metabolism ; *Soil Pollutants/metabolism ; *Copper/toxicity ; *Soil Microbiology ; *Nitrogen/metabolism ; China ; Bacteria/metabolism/genetics/classification ; Soil/chemistry ; Oryza/metabolism/growth &amp; development ; Nitrogen Cycle ; Denitrification ; Microbiota/drug effects ; },
abstract = {The microbiome plays a crucial role in soil nitrogen (N) cycling and in regulating its bioavailability. However, the functional and genomic information of microorganisms encoding N cycling in response to copper (Cu) and cadmium (Cd) contamination is largely unknown. Here, metagenomics and genome binning were used to examine microbial N cycling in Cu and Cd co-contaminated red paddy soils collected from a polluted watershed in southern China. The results showed that soil Cu and Cd concentrations induced more drastic changes in microbial N functional and taxonomic traits than soil general properties. Soil Cu and Cd co-contamination stimulated microbial nitrification, denitrification, and dissimilatory nitrate reduction processes mainly by increasing the abundance of Nitrospira (phylum Nitrospirota), while inhibiting N fixation by decreasing the abundance of Desulfobacca. These contrasting changes in microbial N cycling processes suggested a potential risk of N loss in paddy soils. A high-quality genome was identified as belonging to Nitrospirota with the highest abundance in heavily contaminated soils. This novel Nitrospirota strain possessed metabolic capacities for N transformation and metal resistance. These findings elucidate the genetic mechanisms underlying soil N bioavailability under long-term Cu and Cd contamination, which is essential for maintaining agricultural productivity and controlling heavy metal pollution.},
}
@article {pmid39197244,
year = {2025},
author = {Zhang, C and Gu, C and Wang, M and Chen, J and Chang, H and Chang, Z and Zhou, J and Yue, M and Zhang, W and Zhang, Q and Feng, Z},
title = {Effect of temperature regulation on microbial community, volatile flavours, amino acid profiles, and iridoid glycosides during noni (Morinda citrifolia L.) fruit fermentation.},
journal = {Food chemistry},
volume = {462},
number = {},
pages = {140966},
doi = {10.1016/j.foodchem.2024.140966},
pmid = {39197244},
issn = {1873-7072},
mesh = {*Fermentation ; *Fruit/chemistry/metabolism/microbiology ; *Amino Acids/metabolism/analysis ; *Bacteria/metabolism/classification/genetics/isolation &amp; purification ; *Microbiota ; *Morinda/chemistry/metabolism ; *Iridoid Glycosides/metabolism/analysis/chemistry ; *Temperature ; Volatile Organic Compounds/metabolism/chemistry ; Flavoring Agents/metabolism/chemistry ; },
abstract = {Noni fruit has an unpleasant flavour but is highly bioactive. Therefore, it is necessary to clarify the effect of temperature regulation on quality of fermented noni fruit. In the present study, the formation of flavours, amino acid profiles, and iridoid glycosides during noni fruit fermentation at different temperatures were investigated. We initially found that different temperatures affected core microbial communities. The general evolutionary trends of Acetobacter and Gluconobacter were influenced by different temperatures. Furthermore, high temperature helped maintain low octanoic and hexanoic acids. Subsequently, we found that high temperature improved total amino acids and iridoid glycosides. The correlation network analysis revealed that bacterial communities impacted the quality (volatile flavours, amino acid profiles, and iridoid glycosides) of fermented noni fruit. Overall, altering the temperature induced variations in microbial communities and quality during the noni fruit fermentation process. These results are instrumental in the pursuit of quality control in natural fermentation processes.},
}
@article {pmid39197040,
year = {2024},
author = {Chen, S and Zhang, Z and Liu, S and Chen, T and Lu, Z and Zhao, W and Mou, X and Liu, S},
title = {Consistent signatures in the human gut microbiome of longevous populations.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2393756},
pmid = {39197040},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Longevity ; Aged, 80 and over ; *Feces/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Female ; Adult ; Male ; Aged ; Young Adult ; Metagenomics ; Middle Aged ; Desulfovibrio/genetics/metabolism ; },
abstract = {Gut microbiota of centenarians has garnered significant attention in recent years, with most studies concentrating on the analysis of microbial composition. However, there is still limited knowledge regarding the consistent signatures of specific species and their biological functions, as well as the potential causal relationship between gut microbiota and longevity. To address this, we performed the fecal metagenomic analysis of eight longevous populations at the species and functional level, and employed the Mendelian randomization (MR) analysis to infer the causal associations between microbial taxa and longevity-related traits. We observed that several species including Eisenbergiella tayi, Methanobrevibacter smithii, Hungatella hathewayi, and Desulfovibrio fairfieldensis were consistently enriched in the gut microbiota of long-lived individuals compared to younger elderly and young adults across multiple cohorts. Analysis of microbial pathways and enzymes indicated that E. tayi plays a role in the protein N-glycosylation, while M. smithii is involved in the 3-dehydroquinate and chorismate biosynthesis. Furthermore, H. hathewayi makes a distinct contribution to the purine nucleobase degradation I pathway, potentially assisting the elderly in maintaining purine homeostasis. D. fairfieldensis contributes to the menaquinone (vitamin K2) biosynthesis, which may help prevent age-related diseases such as osteoporosis-induced fractures. According to MR results, Hungatella was significantly positively correlated with parental longevity, and Desulfovibrio also exhibited positive associations with lifespan and multiple traits related to parental longevity. Additionally, Alistipes and Akkermansia muciniphila were consistently enriched in the gut microbiota of the three largest cohorts of long-lived individuals, and MR analysis also suggests their potential causal relationships with longevity. Our findings reveal longevity-associated gut microbial signatures, which are informative for understanding the role of microbiota in regulating longevity and aging.},
}
@article {pmid39196943,
year = {2024},
author = {Rodríguez-Varela, R and Yaka, R and Pochon, Z and Sanchez-Pinto, I and Solaun, JL and Naidoo, T and Guinet, B and Pérez-Ramallo, P and Lagerholm, VK and de Anca Prado, V and Valdiosera, C and Krzewińska, M and Herrasti, L and Azkarate, A and Götherström, A},
title = {Five centuries of consanguinity, isolation, health, and conflict in Las Gobas: A Northern Medieval Iberian necropolis.},
journal = {Science advances},
volume = {10},
number = {35},
pages = {eadp8625},
pmid = {39196943},
issn = {2375-2548},
mesh = {Humans ; Spain ; History, Medieval ; *Consanguinity ; Phylogeny ; Archaeology ; Female ; Male ; Animals ; },
abstract = {Between the 8th and 11th centuries CE, the Iberian Peninsula underwent profound upheaval due to the Umayyad invasion against the Visigoths, resulting in population shifts and lasting demographic impacts. Our understanding of this period is hindered by limited written sources and few archaeogenetic studies. We analyzed 33 individuals from Las Gobas, a necropolis in northern Spain, spanning the 7th to 11th centuries. By combining archaeological and osteological data with kinship, metagenomics, and ancestry analyses, we investigate conflicts, health, and demography of these individuals. We reveal intricate family relationships and genetic continuity within a consanguineous population while also identifying several zoonoses indicative of close interactions with animals. Notably, one individual was infected with a variola virus phylogenetically clustering with the northern European variola complex between ~885 and 1000 CE. Last, we did not detect a significant increase of North African or Middle East ancestries over time since the Islamic conquest of Iberia, possibly because this community remained relatively isolated.},
}
@article {pmid39196507,
year = {2024},
author = {Qian, Y and Sorgen, AA and Steffen, KJ and Heinberg, LJ and Reed, K and Carroll, IM},
title = {Intestinal Energy Harvest Mediates Gut Microbiota-Associated Weight Loss Following Bariatric Surgery.},
journal = {Obesity surgery},
volume = {},
number = {},
pages = {},
pmid = {39196507},
issn = {1708-0428},
support = {1R01DK112585-01//National Institute of Health/ ; 1R01DK112585-01//National Institute of Health/ ; },
abstract = {PURPOSE: Metabolic and bariatric surgery (MBS) is the most effective treatment for class III obesity. The capacity to efficiently extract intestinal energy is potentially a determinant of varying weight loss outcomes post-MBS. Prior research indicated that intestinal energy harvest is correlated with post-MBS weight loss. Studies have also demonstrated that the gut microbiota is associated with weight loss post-MBS. We aim to investigate whether gut microbiota-associated weight loss is mediated by intestinal energy harvest in patients post-MBS.<br><br>MATERIALS AND METHODS: We examined the relationship between specific gut microbiota, intestinal energy harvest, diet, and weight loss using fecal metagenomic sequence data, bomb calorimetry (fecal energy content as a proxy for calorie absorption), and a validated dietary questionnaire on 67 individuals before and after MBS. Mediation analysis and a&#xa0;machine learning algorithm were conducted.<br><br>RESULTS: Intestinal energy harvest was a mediator in the relationship between the&#xa0;intestinal microbiota (Bacteroides caccae) and weight loss outcomes in patients post-MBS at 18&#xa0;months (M). The association between the abundance of B. caccae and post-MBS weight loss rate at 18&#xa0;M was partly mediated by 1&#xa0;M intestinal energy harvest (&#x3b2;&#x2009;=&#x2009;0.001&#x2009;&#xb1;&#x2009;0.001, P&#x2009;=&#x2009;0.020). This mediation represents 2.83% of the total effect (&#x3b2;&#x2009;=&#x2009;0.050&#x2009;&#xb1;&#x2009;0.047; P&#x2009;=&#x2009;0.028). Intestinal microbiota and energy harvest improved random forest model's accuracy in predicting weight loss results.<br><br>CONCLUSION: Energy harvest partly mediates the relationship between the intestinal microbiota and weight loss outcomes among patients post-MBS. This study elucidates a potential mechanism regarding how intestinal energy absorption facilitates the effect of intestinal microbiota on energy metabolism and weight loss outcomes.},
}
@article {pmid39195462,
year = {2024},
author = {Pan, D and Xiao, P and Li, F and Liu, J and Zhang, T and Zhou, X and Zhang, Y},
title = {High Degree of Polymerization of Chitin Oligosaccharides Produced from Shrimp Shell Waste by Enrichment Microbiota Using Two-Stage Temperature-Controlled Technique of Inducing Enzyme Production and Metagenomic Analysis of Microbiota Succession.},
journal = {Marine drugs},
volume = {22},
number = {8},
pages = {},
pmid = {39195462},
issn = {1660-3397},
support = {32100065//National Natural Science Foundation of China/ ; 32300031//National Natural Science Foundation of China/ ; 2023KJ207//Shandong Province Youth Entrepreneurship Technology Support Program for Higher Education Institutions/ ; ZR2023MB095//Natural Science Foundation of Shandong Province of China/ ; },
mesh = {*Chitin/chemistry ; Animals ; *Oligosaccharides/chemistry ; *Microbiota ; *Chitinases/metabolism ; *Animal Shells/chemistry ; Metagenomics/methods ; Temperature ; Polymerization ; Bacteria ; },
abstract = {The direct enzymatic conversion of untreated waste shrimp and crab shells has been a key problem that plagues the large-scale utilization of chitin biological resources. The microorganisms in soil samples were enriched in two stages with powdered chitin (CP) and shrimp shell powder (SSP) as substrates. The enrichment microbiota XHQ10 with SSP degradation ability was obtained. The activities of chitinase and lytic polysaccharide monooxygenase of XHQ10 were 1.46 and 54.62 U/mL. Metagenomic analysis showed that Chitinolyticbacter meiyuanensis, Chitiniphilus shinanonensis, and Chitinimonas koreensis, with excellent chitin degradation performance, were highly enriched in XHQ10. Chitin oligosaccharides (CHOSs) are produced by XHQ10 through enzyme induction and two-stage temperature control technology, which contains CHOSs with a degree of polymerization (DP) more significant than ten and has excellent antioxidant activity. This work is the first study on the direct enzymatic preparation of CHOSs from SSP using enrichment microbiota, which provides a new path for the large-scale utilization of chitin bioresources.},
}
@article {pmid39194557,
year = {2024},
author = {Wang, L and Lu, X and Xing, Z and Teng, X and Wang, S and Liu, T and Zheng, L and Wang, X and Qu, J},
title = {Macrogenomics Reveals Effects on Marine Microbial Communities during Oplegnathus punctatus Enclosure Farming.},
journal = {Biology},
volume = {13},
number = {8},
pages = {},
pmid = {39194557},
issn = {2079-7737},
support = {MEEST-2021-05//The Key Funded with the MNR Key Laboratory of Eco-Environmental Science and Technology, China/ ; 2021CXGC011306//Research and Development Program of Shandong Province, China (Major Science and Technology Innovation Project)/ ; ZR2020MD002//the Natural Science Foundation Shandong Province/ ; 20230304002YY//Science and Technology Major Projects of Jilin Province/ ; Grant SM15B01, SM19B70, and SM19B28//The Doctoral Science Research Foundation of Yantai University/ ; 2320004-SM20RC02//"double-hundred action" of Yantai/ ; },
abstract = {(1) Background: Laizhou Bay is an important aquaculture area in the north of China. Oplegnathus punctatus is one of the species with high economic benefits. In recent years, the water environment of Laizhou Bay has reached a mild eutrophication level, while microorganisms are an important group between the environment and species. In this study, we evaluated alterations in environmental elements, microbial populations, and antibiotic resistance genes (ARGs) along with their interconnections during Oplegnathus punctatus net culture. (2) Methods: A total of 142 samples from various water layers were gathered for metagenome assembly analysis. Mariculture increases the abundance of microorganisms in this culture area and makes the microbial community structure more complex. The change had more significant effects on sediment than on seawater. (3) Results: Certain populations of cyanobacteria and Candidatus Micrarchaecta in seawater, and Actinobacteria and Thaumarchaeota in sediments showed high abundance in the mariculture area. Antibiotic resistance genes in sediments were more sensitive to various environmental factors, especially oxygen solubility and salinity. (4) Conclusions: These findings highlight the complex and dynamic nature of microorganism-environment-ARG interactions, characterized by regional specificity and providing insights for a more rational use of marine resources.},
}
@article {pmid39194508,
year = {2024},
author = {Zhong, Z and An, R and Ma, S and Zhang, N and Zhang, X and Chen, L and Wu, X and Lin, H and Xiang, T and Tan, H and Chen, M},
title = {Association between the Maternal Gut Microbiome and Macrosomia.},
journal = {Biology},
volume = {13},
number = {8},
pages = {},
pmid = {39194508},
issn = {2079-7737},
support = {81773535//National Natural Science Foundation of China/ ; 81973137//National Natural Science Foundation of China/ ; 82173608//National Natural Science Foundation of China/ ; 82360665//National Natural Science Foundation of China/ ; 2018SK2061//Key Research and Development Program of Hunan Province/ ; 2022JJ40343//the Natural Science Foundation of Hunan Province/ ; 21B0513//the Scientific Research Project of Education Department of Hunan Province/ ; 202212053368//the Scientific Research Project of Hunan Provincial Health Commission/ ; },
abstract = {Fetal macrosomia is defined as a birthweight ≥4000 g and causes harm to pregnant women and fetuses. Studies reported that the maternal intestinal microbiome plays a key role in the establishment, growth, and development of the fetal intestinal microbiome. However, whether there is a relationship between maternal gut microbiota and macrosomia remains unclear. Our study aimed to identify gut microbiota that may be related to the occurrence of macrosomia, explore the possible mechanisms by which it causes macrosomia, and establish a prediction model to determine the feasibility of predicting macrosomia by early maternal gut microbiota. We conducted a nested case-control study based on an early pregnancy cohort (ChiCTR1900020652) in the Maternity and Child Health Hospital of Hunan Province on fecal samples of 93 women (31 delivered macrosomia as the case group and 62 delivered normal birth weight newborns as the control group) collected and included in this study. We performed metagenomic analysis to compare the composition and function of the gut microbiome between cases and controls. Correlation analysis was used to explore the association of differential species and differential functional pathways. A random forest model was used to construct an early pregnancy prediction model for macrosomia. At the species level, there were more Bacteroides salyersiae, Bacteroides plebeius, Ruminococcus lactaris, and Bacteroides ovatus in the intestinal microbiome of macrosomias' mothers compared with mothers bearing fetuses that had normal birth weight. Functional pathways of the gut microbiome including gondoate biosynthesis, L-histidine degradation III, cis-vaccenate biosynthesis, L-arginine biosynthesis III, tRNA processing, and mannitol cycle, which were more abundant in the macrosomia group. Significant correlations were found between species and functional pathways. Bacteroides plebeius was significantly associated with the pathway of cis-vaccenate biosynthesis (r = 0.28, p = 0.005) and gondoate biosynthesis (r = 0.28, p < 0.001) and Bacteroides ovatus was positively associated with the pathway of cis-vaccenate biosynthesis (r = 0.29, p = 0.005) and gondoate biosynthesis (r = 0.32, p = 0.002). Bacteroides salyersiae was significantly associated with the pathway of cis-vaccenate biosynthesis (r = 0.24, p = 0.018), gondoate biosynthesis (r = 0.31, p = 0.003), and L-histidine degradation III (r = 0.22, p = 0.291). Finally, four differential species and four clinical indicators were included in the random forest model for predicting macrosomia. The areas under the working characteristic curves of the training and validation sets were 0.935 (95% CI: 0.851~0.979) and 0.909 (95% CI: 0.679~0.992), respectively. Maternal gut microbiota in early pregnancy may play an important role in the development of macrosomia and can be used as potential predictors to prevent macrosomia.},
}
@article {pmid39194269,
year = {2024},
author = {Christians, FC and Akhund-Zade, J and Jarman, K and Venkatasubrahmanyam, S and Noll, N and Blauwkamp, TA and Bercovici, S and Zielinska, A and Carr, AL and Craney, A and Pike, M and Farrell, JJ and Dadwal, S and Wood, JB and Matkovich, E and McAdams, S and Nolte, FS},
title = {Analytical and clinical validation of direct detection of antimicrobial resistance markers by plasma microbial cell-free DNA sequencing.},
journal = {Journal of clinical microbiology},
volume = {},
number = {},
pages = {e0042524},
doi = {10.1128/jcm.00425-24},
pmid = {39194269},
issn = {1098-660X},
abstract = {UNLABELLED: Sequencing of plasma microbial cell-free DNA (mcfDNA) has gained increased acceptance as a valuable adjunct to standard-of-care testing for diagnosis of infections throughout the body. Here, we report the analytical and clinical validation of a novel application of mcfDNA sequencing, the non-invasive detection of seven common antimicrobial resistance (AMR) genetic markers in 18 important pathogens. The AMR markers include SCCmec, mecA, mecC, vanA, vanB, blaCTX-M, and blaKPC. The AMR markers were computationally linked to the pathogens detected. Analytical validation showed high reproducibility (100%), inclusivity (54 to 100%), and exclusivity (100%). Clinical accuracy was assessed with 114 unique plasma samples from patients at seven study sites with concordant culture results for target bacteria from a variety of specimen types and correlated with available phenotypic antimicrobial susceptibility test results and genotypic results. The positive percent agreement (PPA), negative percent agreement (NPA), and diagnostic yield (DY) were estimated for each AMR marker. DY was defined as the percentage of tests that yielded an actionable result of either detected or not detected. The results for the combination of SCCmec and mecA for staphylococci were PPA 19/20 (95.0%), NPA 21/22 (95.4%), DY 42/60 (70.0%); vanA for enterococci were PPA 3/3 (100%), NPA 2/2 (100%), DY 5/6 (83.3%); blaCTX-M for gram-negative bacilli were PPA 5/6 (83.3%), NPA 29/29 (100%), DY 35/49 (71.4%); and blaKPC for gram-negative bacilli were PPA 0/2 (0%), NPA: 23/23 (100%), DY 25/44 (56.8%). The addition of AMR capability to plasma mcfDNA sequencing should provide clinicians with an effective new culture-independent tool for optimization of therapy.<br><br>IMPORTANCE: This manuscript is ideally suited for the Innovative Diagnostic Methods sections as it reports the analytical and clinical validation of a novel application of plasma microbial cell-free DNA sequencing for direct detection of seven selected antimicrobial resistance markers in 18 target pathogens. Clearly, it has potential clinical utility in optimizing therapy and was incorporated into the Karius test workflow in September 2023. In addition, the workflow could readily be adapted to expand the number of target bacteria and antimicrobial resistance markers as needed.},
}
@article {pmid39194141,
year = {2024},
author = {Cruvinel, VRN and Carvalho, E and Alves, DCC and Marques, CP and Bezerra, RDS and Giovanetti, M and Sampaio, SC and Elias, MC and Araújo, WN and Haddad, R and Slavov, SN},
title = {Unveiling microbial worlds: exploring viral metagenomics among waste pickers at Latin America's largest dumpsite.},
journal = {Revista do Instituto de Medicina Tropical de Sao Paulo},
volume = {66},
number = {},
pages = {e49},
pmid = {39194141},
issn = {1678-9946},
mesh = {Humans ; *Metagenomics ; Brazil ; Male ; Adult ; Female ; Viruses/genetics/classification/isolation &amp; purification ; Occupational Exposure ; Case-Control Studies ; Middle Aged ; Refuse Disposal ; },
abstract = {Waste pickers constitute a marginalized demographic engaged in the collection of refuse, facing considerable occupational hazards that heighten their susceptibility to contract infectious diseases. Moreover, waste pickers contend with societal stigmatization and encounter barriers to accessing healthcare services. To explore the viral profile of waste pickers potentially linked to their occupational environment, we conducted a metagenomic analysis on 120 plasma specimens sampled from individuals employed at the Cidade Estrutural dumpsite in Brasilia city, Brazil. In total, 60 blood donors served as a comparative control group. Specimens were pooled and subjected to Illumina NextSeq 2000 sequencing. Viral abundance among waste pickers revealed the presence of significant pathogens, including HIV, HCV, and Chikungunya, which were not detected in the control group. Additionally, elevated levels of anelloviruses and Human pegivirus-1 were noted, with a comparable incidence in the control group. These findings underscore the utility of metagenomics in identifying clinically relevant viral agents within underserved populations. The implications of this study extend to informing public health policies aimed at surveilling infectious diseases among individuals facing socioeconomic disparities and limited access to healthcare resources.},
}
@article {pmid39193958,
year = {2024},
author = {Zhong, Y and Xing, Y},
title = {Diagnosis of Mycobacterium marinum Infection by Metagenomic next-generation sequencing.},
journal = {Clinical laboratory},
volume = {70},
number = {8},
pages = {},
doi = {10.7754/Clin.Lab.2024.240327},
pmid = {39193958},
issn = {1433-6510},
mesh = {Humans ; Female ; *Mycobacterium marinum/isolation &amp; purification/genetics ; *Mycobacterium Infections, Nontuberculous/diagnosis/drug therapy/microbiology ; *High-Throughput Nucleotide Sequencing ; Metagenomics/methods ; Anti-Bacterial Agents/therapeutic use/administration &amp; dosage ; Fingers/microbiology ; Middle Aged ; },
abstract = {BACKGROUND: In December 2023, our hospital confirmed a case of finger infection with Mycobacterium marinum. The patient sought medical attention at our hospital due to a hard scratch on her left middle finger, which was red, swollen, and ulcerated for one month.<br><br>PHYSICAL EXAMINATION: A lesion of approximately 1.5 cm x 2 cm in the patient's left middle finger, surrounded by redness and swelling, unclear boundaries, surface rupture, partial scabbing, and no tenderness during compression. She was treated at the previous clinic, common infectious diseases were considered, and was given intravenous infusion treatment: cefotaxime and clarithromycin, and erythromycin ointment was applied externally. She came to our hospital after poor treatment results. The patient has had hypertension for 3 years, no other systemic diseases, no similar medical history among family members, no history of drug or food allergies.<br><br>METHODS: Clean the wound and remove the scab from the affected area, and use a surgical blade to scrape off necrotic tissue. Send the scraped tissue for pathogen testing: tissue bacterial culture+identification (matrix assisted laser desorption/ionization time-of-flight mass spectrometry, MALDI-TOF), tissue acid fast staining, and tissue metagenomic next-generation sequencing (mNGS). Other auxiliary examinations: blood routine, urine routine, blood fat, liver function, and kidney function.<br><br>RESULTS: Tissue bacterial culture+identification: growth of Mycobacterium marinum; Acid fast staining of tissue: positive; Tissue mNGS: Mycobacterium marinum. Clinical treatment plan: clarithromycin 0.5 g bid po+rifampicin 0.45 g qd po+5-aminolevulinic acid photodynamic therapy (ALA-PDT) qw+boric acid wash wet compress tid. After 14 days of treatment, the area of redness and swelling significantly decreased, and the degree of redness and swelling was significantly reduced compared to admission. The degree of ulcer edge protrusion was also reduced compared to admission. There was a small amount of exudation from the wound, and no necrotic tissue was observed. The patient improved and was discharged.<br><br>CONCLUSIONS: This article reports a case of finger infection with Mycobacterium marinum. Mycobacterium marinum was quickly and accurately identified by mNGS, and reasonable treatment measures were adopted clinically. The patient improved and was discharged. This study has important reference significance for the clinical diagnosis and treatment of Mycobacterium infection. In addition, mNGS as a novel detection method has considerable prospects for rapid diagnosis of pathogens.},
}
@article {pmid39193957,
year = {2024},
author = {Yuan, XH and Chen, QC and Wang, Y and Hao, JH and Guo, AJ and Zhang, JB and Fu, AS and Ge, YL},
title = {Allergic Bronchopulmonary Mycosis with Eosinophilia Caused by Schizophyllum Infection.},
journal = {Clinical laboratory},
volume = {70},
number = {8},
pages = {},
doi = {10.7754/Clin.Lab.2024.240235},
pmid = {39193957},
issn = {1433-6510},
mesh = {Humans ; *Schizophyllum/isolation &amp; purification/genetics ; *Antifungal Agents/therapeutic use ; Eosinophilia/diagnosis/microbiology ; Male ; Bronchoscopy ; High-Throughput Nucleotide Sequencing ; Tomography, X-Ray Computed ; Lung Diseases, Fungal/diagnosis/microbiology/drug therapy ; Middle Aged ; Mycoses/diagnosis/microbiology/drug therapy/complications ; },
abstract = {BACKGROUND: As an opportunistic pathogenic fungus, Schizophyllum has been rarely reported to infect humans. By reporting a case of definite diagnosis of Schizophyllum infection, we aim to improve clinicians' understanding of this bacterium.<br><br>METHODS: By reporting a case with cough and sputum as the main manifestations, after empirical antiinfective chest CT suggesting a more progressive inflammatory lesion and a mass-like lesion in the paratracheal area of the main airways, a diagnosis of Schizophyllum infection was finally made by bronchoscopy with the delivery of metagenomic next-generation sequencing (mNGS).<br><br>RESULTS: The patient was finally diagnosed with rare Schizophyllum infection. After antifungal treatment, the symptoms improved, and the patient was discharged.<br><br>CONCLUSIONS: Although Schizophyllum is a rare fungal infection, it should be taken seriously in patients with diabetes or who are immunocompromised. At the same time, mNGS plays a key role in the detection of rare and emerging pathogens, which is worthy of clinical interest.},
}
@article {pmid39192744,
year = {2024},
author = {Metcalfe-Roach, A and Cirstea, MS and Yu, AC and Ramay, HR and Coker, O and Boroomand, S and Kharazyan, F and Martino, D and Sycuro, LK and Appel-Cresswell, S and Finlay, BB},
title = {Metagenomic Analysis Reveals Large-Scale Disruptions of the Gut Microbiome in Parkinson's Disease.},
journal = {Movement disorders : official journal of the Movement Disorder Society},
volume = {},
number = {},
pages = {},
doi = {10.1002/mds.29959},
pmid = {39192744},
issn = {1531-8257},
support = {GR008160//Pacific Parkinson's Research Institute/ ; FDN-159935/CAPMC/CIHR/Canada ; PPG-2020-0000000052//Parkinson Canada/ ; },
abstract = {BACKGROUND: Parkinson's disease (PD) has been consistently linked to alterations within the gut microbiome.<br><br>OBJECTIVE: Our goal was to identify microbial features associated with PD incidence and progression.<br><br>METHODS: Metagenomic sequencing was used to characterize taxonomic and functional changes to the PD microbiome and to explore their relation to bacterial metabolites and disease progression. Motor and non-motor symptoms were tracked using Movement Disorder Society Unified Parkinson's Disease Rating Scale (MDS-UPDRS) and levodopa equivalent dose across &#x2264;5 yearly study visits. Stool samples were collected at baseline for metagenomic sequencing (176 PD, 100 controls).<br><br>RESULTS: PD-derived stool samples had reduced intermicrobial connectivity and seven differentially abundant species compared to controls. A suite of bacterial functions differed between PD and controls, including depletion of carbohydrate degradation pathways and enrichment of ribosomal genes. Faecalibacterium prausnitzii-specific reads contributed significantly to more than half of all differentially abundant functional terms. A subset of disease-associated functional terms correlated with faster progression of MDS-UPDRS part IV and separated those with slow and fast progression with moderate accuracy within a random forest model (area under curve&#x2009;=&#x2009;0.70). Most PD-associated microbial trends were stronger in those with symmetric motor symptoms.<br><br>CONCLUSION: We provide further evidence that the PD microbiome is characterized by reduced intermicrobial communication and a shift to proteolytic metabolism in lieu of short-chain fatty acid production, and suggest that these microbial alterations may be relevant to disease progression. We also describe how our results support the existence of gut-first versus brain-first PD subtypes. &#xa9; 2024 The Author(s). Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.},
}
@article {pmid39192682,
year = {2024},
author = {Flynn, PJ and Moreau, CS},
title = {Viral diversity and co-evolutionary dynamics across the ant phylogeny.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e17519},
doi = {10.1111/mec.17519},
pmid = {39192682},
issn = {1365-294X},
support = {2210800//Division of Biological Infrastructure/ ; 1900357//Division of Environmental Biology/ ; //National Science Foundation Graduate Research Fellowship Program/ ; },
abstract = {Knowledge of viral biodiversity within insects, particularly within ants, is extremely limited with only a few environmental viruses from invasive ant species identified to date. This study documents and explores the viral communities in ants. We comprehensively profile the metagenomes of a phylogenetically broad group of 35 ant species with varied ecological traits and report the discovery of 3710 novel and unique ant-associated viral genomes. These previously unknown viruses discovered within this study constitute over 95% of all currently described ant viruses, significantly increasing our knowledge of the ant virosphere. The identified RNA and DNA viruses fill gaps in insect-associated viral phylogenies and uncover evolutionary histories characterized by both frequent host switching and co-divergence. Many ants also host diverse bacterial communities, and we discovered that approximately one-third of these new ant-associated viruses are bacteriophages. Two ecological categories, bacterial abundance in the host and habitat degradation are both correlated with ant viral diversity and help to structure viral communities within ants. These data demonstrate that the ant virosphere is remarkably diverse phylogenetically and genomically and provide a substantial foundation for studies in virus ecology and evolution within eukaryotes. We highlight the importance of studying insect-associated viruses in natural ecosystems in order to more thoroughly and effectively understand host-microbe evolutionary dynamics.},
}
@article {pmid39192352,
year = {2024},
author = {Zeng, G and Zeng, L and Wang, Y and Cao, Z and Zeng, X and Xue, Z and Liu, S and Li, Y and He, L},
title = {Correlation between gut microbiota characteristics and non-small cell lung cancer based on macrogenomics sequencing.},
journal = {Hereditas},
volume = {161},
number = {1},
pages = {26},
pmid = {39192352},
issn = {1601-5223},
support = {No. 2023349//Chengdu Municipal Health Commission/ ; },
mesh = {*Carcinoma, Non-Small-Cell Lung/genetics ; Humans ; *Gastrointestinal Microbiome ; *Lung Neoplasms/genetics/microbiology ; Male ; Middle Aged ; Female ; Feces/microbiology ; Aged ; Metagenome ; Metagenomics/methods ; Bacteria/genetics/classification ; },
abstract = {OBJECTIVE: Non-small cell lung cancer (NSCLC) patients undergoing chemotherapy and immunotherapy experience disturbances in the gut microbiota. This study intends to find out the correlation between gut microbiota and clinical indices before and after radiotherapy for NSCLC.<br><br>METHODS: Ten patients with primary NSCLC were screened, and plasma and fecal samples were collected before and after radiotherapy, respectively. Inflammatory indices in plasma were detected. Genomic DNA was extracted from fecal specimens and sequenced on on Illumina HiSeq2000 sequencing platform. Thee sequenced data were subjected to Metagenome assembly, gene prediction, species annotation, and gene function analysis to study and analyze gut microbiota and metabolic functions. The correlation between the diversity of gut microbiota and the clinical indicators of NSCLC patients was evaluated, and the changes of gut microbiota before and after radiotherapy were observed.<br><br>RESULTS: The diversity of gut microbiota in NSCLC patients did not correlate with smoking, pathology, and inflammatory markers. The abundance of phylum (p)_Bacteroidetes increased; p_Firmicutes and p_Bacteroidetes accounted for the highest proportion in NSCLC patients, and the abundance of both was dominantly exchanged after radiotherapy. There was a decrease in genus (g)_Bifidobacterium after radiotherapy in NSCLC patients. There was no significant correlation between the diversity of gut microbiota after radiotherapy and radiotherapy sensitivity, and the structural composition and abundance of gut microbiota remained stable.<br><br>CONCLUSION: The diversity of gut microbiota is altered after radiotherapy in NSCLC patients, showing an increase in harmful bacteria and a decrease in beneficial bacteria.},
}
@article {pmid39192225,
year = {2024},
author = {He, X and Tia, AB and Yin, Q and Gao, L and Wang, L and Tian, T and Xiao, K and Zhang, Y and Tian, F and Ma, X and Harding, D and Dong, X},
title = {A retrospective study revealing complex viral diversity and a substantial burden of HPV infection in SARS-CoV-2 positive individuals, Sierra Leone.},
journal = {Virology journal},
volume = {21},
number = {1},
pages = {201},
pmid = {39192225},
issn = {1743-422X},
support = {2020YFE0205700//National Key Research and Development Program of China/ ; 2022-1G-1131//Capital's Funds for Health Improvement and Research/ ; },
mesh = {Humans ; Sierra Leone/epidemiology ; Retrospective Studies ; *COVID-19/virology/epidemiology ; *Papillomavirus Infections/virology/epidemiology ; *SARS-CoV-2/genetics/isolation &amp; purification/classification ; *Coinfection/virology/epidemiology ; Female ; Adult ; Male ; Middle Aged ; Young Adult ; Nasopharynx/virology ; Adolescent ; Metagenomics ; Phylogeny ; Papillomaviridae/genetics/classification/isolation &amp; purification ; Aged ; Child ; },
abstract = {BACKGROUND: The COVID-19 pandemic has underscored the critical role of sequencing technology in disease control and outbreak response. However, resource limitations and challenging environments often impede such efforts in low and middle-income countries. This study aimed to investigate the spectrum of viral co-infections, particularly with human viral pathogens, in SARS-CoV-2 positive individuals in Sierra Leone using metagenomic sequencing, evaluating the feasibility of utilizing this technology for epidemiological and evolutionary surveillance of pathogens related to public health in low-income environments.<br><br>METHODS: We retrospectively collected and analyzed 98 nasopharyngeal swab specimens from SARS-CoV-2 positive individuals in Sierra Leone. Samples were pre-processed locally and transferred to China via FTA cards for metagenomic sequencing, which was performed using the Novaseq platform. The study focused on the identification of nasopharyngeal viruses co-infecting with SARS-CoV-2, with a deeper analysis of significant human viral pathogens such as HPV.<br><br>RESULTS: The study identified 22 viral taxa from 20 families, including 4 human viruses. Notably, 19.4% of samples showed HPV co-infection with 34 distinct types, predominantly beta and gamma HPVs. Multiple HPV types were found in individual samples, indicating a high complexity of viral co-infections.<br><br>CONCLUSIONS: The identification of a wide range of co-infecting viruses, particularly multiple HPV genotypes, highlights the complexity of viral interactions and their potential implications for public health. These findings enhance our understanding of viral co-infections and provide valuable insights for public health interventions in Sierra Leone. Further research is needed to explore the clinical significance of these findings and their impact on disease outcomes.},
}
@article {pmid39192220,
year = {2024},
author = {Samak, ME and Solyman, SM and Hanora, A and Zakeer, S},
title = {Metagenomic mining of two Egyptian Red Sea sponges associated microbial community.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {315},
pmid = {39192220},
issn = {1471-2180},
support = {59/2020//Academy of Scientific Research and Technology/ ; 6420/2009//SIDA/ ; },
mesh = {*Porifera/microbiology ; Animals ; Indian Ocean ; *Metagenomics ; *Microbiota/genetics ; Egypt ; Bacteria/genetics/classification ; Phylogeny ; Biodiversity ; Multigene Family ; Biological Products/metabolism ; Metagenome ; Proteobacteria/genetics/classification/isolation &amp; purification ; },
abstract = {The Red Sea is a promising habitat for the discovery of new bioactive marine natural products. Sponges associated microorganisms represent a wealthy source of compounds with unique chemical structures and diverse biological activities. Metagenomics is an important omics-based culture-independent technique that is used as an effective tool to get genomic and functional information on sponge symbionts. In this study, we used metagenomic analysis of two Egyptian Red Sea sponges Hyrtios erectus and Phorbas topsenti microbiomes to study the biodiversity and the biosynthetic potential of the Red Sea sponges to produce bioactive compounds. Our data revealed high biodiversity of the two sponges' microbiota with phylum Proteobacteria as the most dominant phylum in the associated microbial community with an average of 31% and 70% respectively. The analysis also revealed high biosynthetic potential of sponge Hyrtios erectus microbiome through detecting diverse types of biosynthetic gene clusters (BGCs) with predicted cytotoxic, antibacterial and inhibitory action. Most of these BGCs were predicted to be novel as they did not show any similarity with any MIBiG database known cluster. This study highlights the importance of the microbiome of the collected Red Sea sponge Hyrtios erectus as a valuable source of new bioactive natural products.},
}
@article {pmid39191812,
year = {2024},
author = {Feng, Y and Wei, R and Chen, Q and Shang, T and Zhou, N and Wang, Z and Chen, Y and Chen, G and Zhang, G and Dong, K and Zhong, Y and Zhao, H and Hu, F and Zheng, H},
title = {Host specificity and cophylogeny in the "animal-gut bacteria-phage" tripartite system.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {72},
pmid = {39191812},
issn = {2055-5008},
mesh = {Animals ; *Host Specificity ; *Bacteriophages/genetics/physiology ; *Gastrointestinal Microbiome ; Bees/virology/microbiology ; *Bacteria/virology/genetics/classification ; *Phylogeny ; Metagenomics/methods ; Metagenome ; },
abstract = {Cophylogeny has been identified between gut bacteria and their animal host and is highly relevant to host health, but little research has extended to gut bacteriophages. Here we use bee model to investigate host specificity and cophylogeny in the "animal-gut bacteria-phage" tripartite system. Through metagenomic sequencing upon different bee species, the gut phageome revealed a more variable composition than the gut bacteriome. Nevertheless, the bacteriome and the phageome showed a significant association of their dissimilarity matrices, indicating a reciprocal interaction between the two kinds of communities. Most of the gut phages were host generalist at the viral cluster level but host specialist at the viral OTU level. While the dominant gut bacteria Gilliamella and Snodgrassella exhibited matched phylogeny with bee hosts, most of their phages showed a diminished level of cophylogeny. The evolutionary rates of the bee, the gut bacteria and the gut phages showed a remarkably increasing trend, including synonymous and non-synonymous substitution and gene content variation. For all of the three codiversified tripartite members, however, their genes under positive selection and genes involving gain/loss during evolution simultaneously enriched the functions into metabolism of nutrients, therefore highlighting the tripartite coevolution that results in an enhanced ecological fitness for the whole holobiont.},
}
@article {pmid39191760,
year = {2024},
author = {Hartikainen, AK and Jalanka, J and Lahtinen, P and Ponsero, AJ and Mertsalmi, T and Finnegan, L and Crispie, F and Cotter, PD and Arkkila, P and Satokari, R},
title = {Fecal microbiota transplantation influences microbiota without connection to symptom relief in irritable bowel syndrome patients.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {73},
pmid = {39191760},
issn = {2055-5008},
support = {316338//Academy of Finland (Suomen Akatemia)/ ; 323156//Academy of Finland (Suomen Akatemia)/ ; },
mesh = {*Irritable Bowel Syndrome/therapy/microbiology ; Humans ; *Fecal Microbiota Transplantation/methods ; *RNA, Ribosomal, 16S/genetics ; Female ; Male ; Adult ; Treatment Outcome ; *Gastrointestinal Microbiome ; Middle Aged ; Feces/microbiology ; Metagenomics/methods ; Bacteria/classification/genetics/isolation &amp; purification ; },
abstract = {Imbalanced microbiota may contribute to the pathophysiology of irritable bowel syndrome (IBS), thus fecal microbiota transplantation (FMT) has been suggested as a potential treatment. Previous studies on the relationship between clinical improvement and microbiota after FMT have been inconclusive. In this study, we used 16S rRNA gene amplicon and shotgun metagenomics data from a randomized, placebo controlled FMT trial on 49 IBS patients to analyze changes after FMT in microbiota composition and its functional potential, and to identify connections between microbiota and patients' clinical outcome. As a result, we found that the successful modulation of microbiota composition and functional profiles by FMT from a healthy donor was not associated with the resolution of symptoms in IBS patients. Notably, a donor derived strain of Prevotella copri dominated the microbiota in those patients in the FMT group who had a low relative abundance of P. copri pre-FMT. The results highlight the multifactorial nature of IBS and the role of recipient's microbiota in the colonization of donor's strains.},
}
@article {pmid39191378,
year = {2024},
author = {da Silva, VG and Smith, NW and Mullaney, JA and Wall, C and Roy, NC and McNabb, WC},
title = {Food-breastmilk combinations alter the colonic microbiome of weaning infants: an in silico study.},
journal = {mSystems},
volume = {9},
number = {9},
pages = {e0057724},
pmid = {39191378},
issn = {2379-5077},
support = {//High-Value Nutrition National Science Challenge/ ; },
mesh = {Humans ; *Milk, Human/chemistry/microbiology/metabolism ; *Gastrointestinal Microbiome/physiology ; Infant ; *Weaning ; *Colon/microbiology/metabolism ; *Computer Simulation ; Fatty Acids, Volatile/metabolism/analysis ; },
abstract = {The introduction of solid foods to infants, also known as weaning, is a critical point for the development of the complex microbial community inhabiting the human colon, impacting host physiology in infancy and later in life. This research investigated in silico the impact of food-breastmilk combinations on growth and metabolite production by colonic microbes of New Zealand weaning infants using the metagenome-scale metabolic model named Microbial Community. Eighty-nine foods were individually combined with breastmilk, and the 12 combinations with the strongest influence on the microbial production of short-chain fatty acids (SCFAs) and branched-chain fatty acids (BCFAs) were identified. Fiber-rich and polyphenol-rich foods, like pumpkin and blackcurrant, resulted in the greatest increase in predicted fluxes of total SCFAs and individual fluxes of propionate and acetate when combined, respectively, with breastmilk. Identified foods were further combined with other foods and breastmilk, resulting in 66 multiple food-breastmilk combinations. These combinations altered in silico the impact of individual foods on the microbial production of SCFAs and BCFAs, suggesting that the interaction between the dietary compounds composing a meal is the key factor influencing colonic microbes. Blackcurrant combined with other foods and breastmilk promoted the greatest increase in the production of acetate and total SCFAs, while pork combined with other foods and breastmilk decreased the production of total BCFAs.IMPORTANCELittle is known about the influence of complementary foods on the colonic microbiome of weaning infants. Traditional in vitro and in vivo microbiome methods are limited by their resource-consuming concerns. Modeling approaches represent a promising complementary tool to provide insights into the behavior of microbial communities. This study evaluated how foods combined with other foods and human milk affect the production of short-chain fatty acids and branched-chain fatty acids by colonic microbes of weaning infants using a rapid and inexpensive in silico approach. Foods and food combinations identified here are candidates for future experimental investigations, helping to fill a crucial knowledge gap in infant nutrition.},
}
@article {pmid39191330,
year = {2024},
author = {Wang, H and Ma, X and Ran, X and Wang, T and Zhou, M and Liu, C and Li, X and Wu, M and Wang, Y},
title = {Analyzing performance and microbial mechanisms in an incineration leachate treatment after waste separation: Integrated metagenomic and metaproteomic analyses.},
journal = {The Science of the total environment},
volume = {951},
number = {},
pages = {175821},
doi = {10.1016/j.scitotenv.2024.175821},
pmid = {39191330},
issn = {1879-1026},
mesh = {*Water Pollutants, Chemical/analysis ; *Biodegradation, Environmental ; *Metagenomics ; Incineration ; Waste Disposal, Fluid/methods ; Nitrification ; Nitrogen ; Proteomics ; },
abstract = {The absence of food waste after separation poses a significant challenge to incineration leachate treatment, as it decreases the C/N ratio and COD of leachate, greatly impacting the biological treatment process. A one-year in-situ study was systematically conducted in an incineration leachate treatment plant that experienced waste separation, focusing on the variations in carbon and nitrogen removal performance as well as the involved microbial mechanism of the "anaerobic digestion (AD) + two-stage A/O" process. Results indicated that the biodegradability of leachate significantly decreased over time, with COD concentration decreasing by 10 times and the average C/N ratio decreasing from 12.3 to 1.4. The AD process was maintained stable, achieving a COD removal efficiency exceeding 92 %. The nitrification process also remained stable; while the denitrification process was significantly affected, and a nine-fold increase in external glucose addition was required to achieve a nitrogen removal efficiency of 85 %. Metagenomic analysis indicated that comammox Nitrospira (contributing 90 % to ammonia monooxygenase) occupied the dominant position over Nitrosomonas for nitrification due to the low NH4[+]-N concentration in A/O tanks (<35 mg/L), and Methanothrix was substituted by Methanosarcina for methanogenesis in AD unit. Metaproteomic results further elucidated that the expression of enzymes responsible for denitrification process, i.e., Nir, Nor, Nos (convert NO2[-] to N2), was decreased significantly, although the expression of enzymes related to glycolysis and TCA cycle were stimulated by glucose addition. The expression of Nar (convert NO3[-]-N to NO2[-]-N) remained stable, while the imbalance expression within denitrifying enzymes might have facilitated occurrence of partial denitrification, attributed to the low C/N ratio. The results prove that the function robustness and metabolic versatility were achieved in leachate treatment plant after waste separation but at the cost of the high external carbon resource addition, highlighting the urgent requirement for low-carbon nitrogen removal technologies.},
}
@article {pmid39191326,
year = {2024},
author = {Chen, Y and Wang, F and Gao, J and He, X and Liu, Q and Liu, L},
title = {Enhancing bioremediation of petroleum-contaminated soil by sophorolipids-modified biochar: Combined metagenomic and metabolomic analyses.},
journal = {The Science of the total environment},
volume = {951},
number = {},
pages = {175772},
doi = {10.1016/j.scitotenv.2024.175772},
pmid = {39191326},
issn = {1879-1026},
mesh = {*Biodegradation, Environmental ; *Charcoal/chemistry ; *Petroleum/metabolism ; *Soil Pollutants/metabolism ; *Soil Microbiology ; *Metabolomics ; Metagenomics ; },
abstract = {In this study, sophorolipids (SLs)-modified biochar (BC-SLs) was used to enhance the bioremediation of petroleum hydrocarbons (PHs) contaminated soil. The biodegradation rate of petroleum hydrocarbons (PHs) by BC-SLs and BC treatments were 62.86 % and 52.64 % after 60 days of remediation experiments, respectively, higher than non-biochar treatment group (24.09 %). The metagenomic analysis showed that the abundance of petroleum-degrading bacteria Actinobacteria and Proteobacteria were increased by 3.8 % and 5.3 %, respectively in BC-SLs treatment, and the abundance of functional genes for PHs degradation, such as alkB, nidA and pcaG, were significantly increased by 12.85 %, 30.08 % and 21.01 %, respectively. The metabolomic analysis showed that BC-SLs facilitated the metabolic process of PHs, the microbial metabolism of petroleum hydrocarbons (PHs) became more active. Fatty acid degradation and polycyclic aromatic hydrocarbons (PAHs) degradation were up-regulated, indicating the promoting effect of the BC-SLs for PHs metabolism. The combined metagenomic and metabolomic analysis demonstrated the strong positive correlations between PHs metabolites and PHs-degrading bacteria, such as lauric acid vs. Actinobacteria, benzoic vs. Proteobacteria. The strong positive correlations between PHs metabolites and PHs-degrading genes were also observed, such as o-ehyltoluene vs. nahD, 4-isopropylbenzoic acid vs. etbAa. The modification of biochar with SLs increased the oxygen-containing functional groups on the surface of biochar. Meanwhile, the emulsification and solubilization of SLs promoted the bioavailability of PHs. The effects of BC-SLs on the nitrogen cycle during PHs remediation showed that it facilitated the accumulation of nitrogen-fixing genes, promoted nitrification but inhibited denitrification process. This study confirms that the application of BC-SLs is an effective remediation of PHs contamination and a sustainable method for controlling agricultural waste resources.},
}
@article {pmid39190031,
year = {2024},
author = {Li, X and Zheng, T and Xiao, Y and Zhao, Y and Wu, P},
title = {Field-Deployable Colorimetric Array for On-Site Diagnosis of Urinary Tract Infection and Identification of Causative Pathogens.},
journal = {Analytical chemistry},
volume = {96},
number = {36},
pages = {14679-14687},
doi = {10.1021/acs.analchem.4c03617},
pmid = {39190031},
issn = {1520-6882},
mesh = {*Urinary Tract Infections/diagnosis/microbiology ; *Colorimetry ; Humans ; *Polymerase Chain Reaction ; DNA, Bacterial/analysis ; },
abstract = {Urinary tract infection (UTI) is a common and prevalent disease caused by a spectrum of pathogens. Lack of access to rapid, portable, and high-quality diagnostics in resource-limited settings aggravates the improper treatment of UTIs, which is also a major driver of antibiotic misuse worldwide. Here, we describe a custom-made portable colorimetric array (PoCA) for reading out polymerase chain reaction (PCR) amplicons, the rationale of which is to transfer the previously developed dsDNA-based photosensitization colorimetric assay (solution) onto paper discs for detection. By integrating mini-LED irradiation and paper discs, the PoCA can read out 96 PCR tests in one pot, thus allowing diagnosis and identification of 12 prevailing UTI pathogens in less than 2 h, coupled with a portable thermal cycler for PCR. After analyzing 200 clinical urine samples, the pathogen profiling accuracy of the PoCA was demonstrated to be higher than the standard urine culture (confirmed with metagenomic next-generation sequencing). The PoCA platform could be used in primary care for rapid UTI diagnosis and pathogen identification.},
}
@article {pmid39189780,
year = {2024},
author = {Liu, L and He, X and Wang, J and Li, M and Wei, X and Yang, J and Cheng, G and Du, W and Liu, Z and Xiao, X},
title = {Exploring the associations between gut microbiota composition and SARS-CoV-2 inactivated vaccine response in mice with type 2 diabetes mellitus.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0038024},
doi = {10.1128/msphere.00380-24},
pmid = {39189780},
issn = {2379-5042},
abstract = {UNLABELLED: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccination is crucial for protecting vulnerable individuals, yet individuals with type 2 diabetes mellitus (T2DM) often exhibit impaired vaccine responses. Emerging evidence suggests that the composition of the host microbiota, crucial in immune regulation and development, influences vaccine efficacy. This study aimed to characterize the relationships between the SARS-CoV-2 inactivated vaccine and the host microbiota (specifically, gut and lung microbiota) of C57BL/6 mice with T2DM. Employing 16S rRNA metagenomic sequencing and ultra-high-performance liquid chromatography-mass spectrometry, we observed lower alpha diversity and distinct beta diversity in fecal microbiota before vaccination and in gut microbiota 28 days post-vaccination between T2DM mice and healthy mice. Compared with healthy mice, T2DM mice showed a higher Firmicutes/Bacteroidetes ratio 28 days post-vaccination. Significant alterations in gut microbiota composition were detected following vaccination, while lung microbiota remained unchanged. T2DM was associated with a diminished initial IgG antibody response against the spike protein, which subsequently normalized after 28 days. Notably, the initial IgG response positively correlated with fecal microbiota alpha diversity pre-vaccination. Furthermore, after 28 days, increased relative abundance of gut probiotics (Bifidobacterium and Lactobacillus) and higher levels of the gut bacterial tryptophan metabolite, indole acrylic acid, were positively associated with IgG levels. These findings suggest a potential link between vaccine efficacy and gut microbiota composition. Nonetheless, further research is warranted to elucidate the precise mechanisms underlying the impact of the gut microbiome on vaccine response. Overall, this study enhances our understanding of the intricate relationships among host microbiota, SARS-CoV-2 vaccination, and T2DM, with potential implications for improving vaccine efficacy.<br><br>IMPORTANCE: Over 7 million deaths attributed to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by 6 May 2024 underscore the urgent need for effective vaccination strategies. However, individuals with type 2 diabetes mellitus (T2DM) have been identified as particularly vulnerable and display compromised immune responses to vaccines. Concurrently, increasing evidence suggests that the composition and diversity of gut microbiota, crucial regulators of immune function, may influence the efficacy of vaccines. Against this backdrop, our study explores the complex interplay among SARS-CoV-2 inactivated vaccination, T2DM, and host microbiota. We discover that T2DM compromises the initial immune response to the SARS-CoV-2 inactivated vaccine, and this response is positively correlated with specific features of the gut microbiota, such as alpha diversity. We also demonstrate that the vaccination itself induces alterations in the composition and structure of the gut microbiota. These findings illuminate potential links between the gut microbiota and vaccine efficacy in individuals with T2DM, offering valuable insights that could enhance vaccine responses in this high-risk population.},
}
@article {pmid39189742,
year = {2024},
author = {Wurzbacher, CE and Hammer, J and Haufschild, T and Wiegand, S and Kallscheuer, N and Jogler, C},
title = {"Candidatus Uabimicrobium helgolandensis"-a planctomycetal bacterium with phagocytosis-like prey cell engulfment, surface-dependent motility, and cell division.},
journal = {mBio},
volume = {},
number = {},
pages = {e0204424},
doi = {10.1128/mbio.02044-24},
pmid = {39189742},
issn = {2150-7511},
abstract = {The unique cell biology presented by members of the phylum Planctomycetota has puzzled researchers ever since their discovery. Initially thought to have eukaryotic-like features, their traits are now recognized as exceptional but distinctly bacterial. However, recently discovered strains again added novel and stunning aspects to the planctomycetal cell biology-shapeshifting by members of the "Saltatorellus" clade to an extent that is unprecedented in any other bacterial phylum, and phagocytosis-like cell engulfment in the bacterium "Candidatus Uabimicrobium amorphum." These recent additions to the phylum Planctomycetota indicate hitherto unexplored members with unique cell biology, which we aimed to make accessible for further investigations. Targeting bacteria with features like "Ca. U. amorphum", we first studied both the morphology and behavior of this microorganism in more detail. While similar to eukaryotic amoeboid organisms at first sight, we found "Ca. U. amorphum" to be rather distinct in many regards. Presenting a detailed description of "Ca. U. amorphum," we furthermore found this organism to divide in a fashion that has never been described in any other organism. Employing the obtained knowledge, we isolated a second "bacterium of prey" from the harbor of Heligoland Island (North Sea, Germany). Our isolate shares key features with "Ca. U. amorphum": phagocytosis-like cell engulfment, surface-dependent motility, and the same novel mode of cell division. Being related to "Ca. U. amorphum" within genus thresholds, we propose the name "Ca. Uabimicrobium helgolandensis" for this strain.IMPORTANCE"Candidatus Uabimicrobium helgolandensis" HlEnr_7 adds to the explored bacterial biodiversity with its phagocytosis-like uptake of prey bacteria. Enrichment of this strain indicates that there might be "impossible" microbes out there, missed by metagenomic analyses. Such organisms have the potential to challenge our understanding of nature. For example, the origin of eukaryotes remains enigmatic, with a contentious debate surrounding both the mitochondrial host entity and the moment of uptake. Currently, favored models involve a proteobacterium as the mitochondrial progenitor and an Asgard archaeon as the fusion partner. Models in which a eukaryotic ancestor engulfed the mitochondrial ancestor via phagocytosis had been largely rejected due to bioenergetic constraints. Thus, the phagocytosis-like abilities of planctomycetal bacteria might influence the debate, demonstrating that prey engulfment is possible in a prokaryotic cellular framework.},
}
@article {pmid39189724,
year = {2024},
author = {Xiao, JZ and Nesbø, CL and Molenda, O and Toth, CRA and Edwards, EA},
title = {Draft genome of an anaerobic nitrate-reducing, benzene-degrading member of the order Thermincolales.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0029524},
doi = {10.1128/mra.00295-24},
pmid = {39189724},
issn = {2576-098X},
abstract = {We present a metagenome assembled genome (MAG) of an anaerobic bacterium from a nitrate-reducing, benzene-degrading enrichment culture (NRBC). The draft Thermincolales genome consists of 20 contigs with a total length of 4.09 Mbp and includes putative carboxylase genes likely involved in benzene activation.},
}
@article {pmid39189169,
year = {2024},
author = {Hejazirad, SP and de Abreu, CM and Carneiro, GHF and Gomes, CR and Spinola Filho, PRC and da Costa, MR and Santos, JBD},
title = {The Impact of Metolachlor Applications and Phytoremediation Processes on Soil Microorganisms: Insights from Functional Metagenomics Analysis.},
journal = {Journal of xenobiotics},
volume = {14},
number = {3},
pages = {970-988},
pmid = {39189169},
issn = {2039-4713},
support = {PQD//National Council for Scientific and Technological Development/ ; 00097-22//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de Minas Gerais/ ; 001//Coordena&#xe7;&#xe3;o de Aperfeicoamento de Pessoal de N&#xed;vel Superior/ ; },
abstract = {This study assessed the impact of phytoremediation on reducing the residual concentration of metolachlor in soil treated with doses of 530.7 and 1061.4 g/ha and its effect on microbial biodiversity in contaminated areas. For the plant species Avena sativa and Medicago sativa, a significant efficacy of 54.5 and 36.4% was observed in the dissipation of the herbicide, especially at higher doses. Although metolachlor application reduced soil microbial biodiversity, phytoremediating plants, especially M. sativa, promoted greater richness and distribution of microbial species, mitigating the negative effects of the herbicide. Principal component analysis revealed the influence of these plants and metolachlor on the composition of the microbial community. These results highlight the importance of phytoremediation in promoting soil biodiversity and reducing herbicide contamination, providing crucial insights for remediation strategies in contaminated areas.},
}
@article {pmid39189041,
year = {2024},
author = {Haussmann, AJ and McMahan, ZH and Volkmann, ER},
title = {Understanding the gastrointestinal microbiome in systemic sclerosis: methodological advancements and emerging research.},
journal = {Current opinion in rheumatology},
volume = {},
number = {},
pages = {},
doi = {10.1097/BOR.0000000000001048},
pmid = {39189041},
issn = {1531-6963},
abstract = {PURPOSE OF REVIEW: This review highlights the role of the gastrointestinal (GI) microbiome in systemic sclerosis (SSc). We describe techniques for evaluating the GI microbiome in humans, and emerging research linking GI microbiome alterations (i.e., dysbiosis) and distinct SSc clinical manifestations. We also address the evolving treatment landscape targeting dysbiosis in SSc.<br><br>RECENT FINDINGS: Recent literature brings into focus the complex relationship between the GI microbiome and SSc pathogenesis. Advanced techniques (e.g., shotgun metagenomics, meta-transcriptomics) provide deeper insights into microbial taxonomy and active gene expression, exposing dysbiosis as a potential driver of SSc. New studies demonstrate that SSc patients who possess specific SSc clinical features, (e.g., interstitial lung disease), have unique GI microbiome profiles.<br><br>SUMMARY: Dysbiosis is associated with specific clinical features in patients with SSc. New tools for studying the GI microbiome have furthered our understanding of the relationship between dysbiosis and SSc complications. Therapeutic avenues such as dietary adjustments, probiotics, antibiotics, mindfulness practices, and fecal transplants offer potential for managing SSc and preventing its progression through GI microbiome modulation. By clarifying what is known about the relationship between the GI dysbiosis, GI dysfunction, and SSc, this review enhances our understanding of SSc pathogenesis and proposes targeted interventions.},
}
@article {pmid39187935,
year = {2024},
author = {Versi, A and Azim, A and Ivan, FX and Abdel-Aziz, MI and Bates, S and Riley, J and Uddin, M and Zounemat Kermani, N and Maitland-Van Der Zee, AH and Dahlen, SE and Djukanovic, R and Chotirmall, SH and Howarth, P and Adcock, IM and Chung, KF and , },
title = {A severe asthma phenotype of excessive airway Haemophilus influenzae relative abundance associated with sputum neutrophilia.},
journal = {Clinical and translational medicine},
volume = {14},
number = {9},
pages = {e70007},
pmid = {39187935},
issn = {2001-1326},
support = {115010//Innovative Medicines Initiative/ ; FP7/2007-2013//European Union Seventh Framework Programme/ ; //European Federation of Pharmaceutical Industries and Associations/ ; //UK Research and Innovation/ ; //BBSRC/ ; },
mesh = {Humans ; *Asthma/microbiology ; *Haemophilus influenzae/pathogenicity/genetics ; *Sputum/microbiology ; Male ; Female ; Adult ; *Neutrophils/metabolism ; Middle Aged ; Phenotype ; Haemophilus Infections/microbiology ; },
abstract = {BACKGROUND: Severe asthma (SA) encompasses several clinical phenotypes with a heterogeneous airway microbiome. We determined the phenotypes associated with a low α-diversity microbiome.<br><br>METHODS: Metagenomic sequencing was performed on sputum samples from SA participants. A threshold of 2 standard deviations below the mean of &#x3b1;-diversity of mild-moderate asthma and healthy control subjects was used to define those with an abnormal abundance threshold as relative dominant species (RDS).<br><br>FINDINGS: Fifty-one out of 97 SA samples were classified as RDSs with Haemophilus influenzae RDS being most common (n&#xa0;=&#xa0;16), followed by Actinobacillus unclassified (n&#xa0;=&#xa0;10), Veillonella unclassified (n&#xa0;=&#xa0;9), Haemophilus aegyptius (n&#xa0;=&#xa0;9), Streptococcus pseudopneumoniae (n&#xa0;=&#xa0;7), Propionibacterium acnes (n&#xa0;=&#xa0;5), Moraxella catarrhalis (n&#xa0;=&#xa0;5) and Tropheryma whipplei (n&#xa0;=&#xa0;5). Haemophilus influenzae RDS had the highest duration of disease, more exacerbations in previous year and greatest number on daily oral corticosteroids. Hierarchical clustering of RDSs revealed a C2 cluster (n&#xa0;=&#xa0;9) of highest relative abundance of exclusively Haemophilus influenzae RDSs with longer duration of disease and higher sputum neutrophil counts associated with enrichment pathways of MAPK, NF-&#x3ba;B, TNF, mTOR and necroptosis, compared to the only other cluster, C1, which consisted of 7 Haemophilus influenzae RDSs out of 42. Sputum transcriptomics of C2 cluster compared to C1 RDSs revealed higher expression of neutrophil extracellular trap pathway (NETosis), IL6-transignalling signature and neutrophil activation.<br><br>CONCLUSION: We describe a Haemophilus influenzae cluster of the highest relative abundance associated with neutrophilic inflammation and NETosis indicating a host response to the bacteria. This phenotype of severe asthma may respond to specific antibiotics.},
}
@article {pmid39187802,
year = {2024},
author = {Anitua, E and Murias-Freijo, A and Tierno, R and Tejero, R and Alkhraisat, MH},
title = {Assessing peri-implant bacterial community structure: the effect of microbiome sample collection method.},
journal = {BMC oral health},
volume = {24},
number = {1},
pages = {1001},
pmid = {39187802},
issn = {1472-6831},
mesh = {Humans ; *Microbiota ; *Biofilms ; *Gingival Crevicular Fluid/microbiology ; *Dental Implants/microbiology ; Middle Aged ; Specimen Handling/methods ; Female ; Male ; High-Throughput Nucleotide Sequencing ; Bacteria/classification/isolation &amp; purification ; Aged ; },
abstract = {BACKGROUND: Oral microbiota comprises polymicrobial communities shaped by mutualistic coevolution with the host, contributing to homeostasis and regulating immune function. Nevertheless, dysbiosis of oral bacterial communities is associated with a number of clinical symptoms that ranges from infections to oral cancer. Peri-implant diseases are biofilm-associated inflammatory conditions affecting the soft and hard tissues around dental implants. Characterization and identification of the biofilm community are essential for the understanding of the pathophysiology of such diseases. For that sampling methods should be representative of the biofilm communities Therefore, there is a need to know the effect of different sampling strategies on the biofilm characterization by next generation sequencing.<br><br>METHODS: With the aim of selecting an appropriate microbiome sampling procedure for periimplant biofilms, next generation sequencing was used for characterizing the bacterial communities obtained by three different sampling strategies two months after transepithelial abutment placement: adjacent periodontal crevicular fluid (ToCF), crevicular fluid from transepithelial abutment (TACF) and transepithelial abutment (TA).<br><br>RESULTS: Significant differences in multiple alpha diversity indices were detected at both the OTU and the genus level between different sampling procedures. Differentially abundant taxa were detected between sample collection strategies, including peri-implant health and disease related taxa. At the community level significant differences were also detected between TACF and TA and also between TA and ToCF. Moreover, differential network properties and association patterns were identified.<br><br>CONCLUSIONS: The selection of sample collection strategy can significantly affect the community composition and structure.<br><br>TRIAL REGISTRATION: This research is part of a randomized clinical trial that was designed to assess the effect of transepithelial abutment surface on the biofilm formation. The trial was registered at Trial Registration ClinicalTrials.gov under the number NCT03554876.},
}
@article {pmid39187328,
year = {2024},
author = {Yeh, TK and Huang, YT and Liu, PY and Mao, YC and Lai, CS and Lai, KL and Tseng, CH and Liu, CW and Huang, WH and Huang, HP and Lin, KP},
title = {Pathogenic Detection by Metagenomic Next-generation Sequencing in Skin and Soft Tissue Infection.},
journal = {In vivo (Athens, Greece)},
volume = {38},
number = {5},
pages = {2364-2373},
pmid = {39187328},
issn = {1791-7549},
mesh = {Humans ; *Soft Tissue Infections/microbiology/diagnosis ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Male ; Female ; Middle Aged ; Aged ; Adult ; Bacteria/genetics/isolation &amp; purification/classification ; Metagenome ; Aged, 80 and over ; },
abstract = {BACKGROUND/AIM: Skin and soft tissue infections (SSTIs) can be life-threatening, but the conventional bacterial cultures have low sensitivity and are time-consuming. Metagenomic next-generation sequencing (mNGS) is widely used as a diagnostic tool for detecting pathogens from infection sites. However, the use of mNGS for pathogen detection in SSTIs and related research is still relatively limited.<br><br>PATIENTS AND METHODS: From January 2020 to October 2021, 19 SSTI samples from 16 patients were collected in a single center (Taichung Veterans General Hospital, Taichung, Taiwan). The clinical samples were simultaneously subjected to mNGS and conventional bacterial culture methods to detect pathogens. Clinical characteristics were prospectively collected through electronic chart review. The microbiological findings from conventional bacterial culture and mNGS were analyzed and compared.<br><br>RESULTS: The mNGS method detected a higher proportion of multiple pathogens in SSTIs compared to conventional bacterial culture methods. Pseudomonas spp. was among the most commonly identified Gram-negative bacilli using mNGS. Additionally, the mNGS method identified several rare pathogens in patients with SSTIs, including Granulicatella adiacens, Bacillus thuringiensis, and Bacteroides fragilis. Antimicrobial resistance genes were detected in 10 samples (52.6%) using the mNGS method, including genes for extended-spectrum beta-lactamase, Ambler class C &#x3b2;-lactamases, and carbapenemase.<br><br>CONCLUSION: mNGS not only plays an important role in the detection of pathogens in soft tissue infections, but also informs clinical professionals about the presence of additional microbes that may be important for treatment decisions. Further studies comparing conventional pathogen culture with the mNGS method in SSTIs are required.},
}
@article {pmid39186902,
year = {2024},
author = {Pan, Y and Zeng, J and Zhang, L and Hu, J and Hao, H and Zeng, Z and Li, Y},
title = {The fate of antibiotics and antibiotic resistance genes in Large-Scale chicken farm Environments: Preliminary view of the performance of National veterinary Antimicrobial use reduction Action in Guangdong, China.},
journal = {Environment international},
volume = {191},
number = {},
pages = {108974},
doi = {10.1016/j.envint.2024.108974},
pmid = {39186902},
issn = {1873-6750},
mesh = {*Chickens ; Animals ; China ; *Anti-Bacterial Agents/pharmacology ; *Farms ; *Drug Resistance, Microbial/genetics ; Drug Resistance, Bacterial/genetics ; Animal Husbandry ; Genes, Bacterial ; Escherichia coli/drug effects/genetics ; },
abstract = {In 2018, China implemented the Veterinary Antimicrobial Use Reduction Action to curb the rapid development of antibiotic resistance (AR). However, the AR-related pollutions in animal farms after the reduction policy has been poorly investigated. Here, we performed a comprehensive investigation combining UPLC-MS/MS, metagenomic, and bacterial genomic analyses in eight representative large-scale chicken farms in Guangdong, China. Our results showed that antibiotics and ARGs contaminations were more severe in broiler farms than in layer farms. Notably, diverse tet(X) variants were prevalent in the chicken farms. These tet(X)s was carried by diverse E. coli lineages and obviously correlated with ISCR2 and IS1B transposases. The resistomes in chicken farms was significantly correlated with microbial community, and multiple factor analyses indicated that the joint effect of antibiotics-microbial community-MGEs was the most dominant driver of ARGs. Host tracking identified a variety of ARG bacterial hosts and the co-occurrence of ARGs-MRGs-MGEs. Source tracking indicated that the inherent component represented the main feature of resistomes in different hosts, while ARG transfer between the chicken gut and farm environments were frequent. A multiperspective evaluation of AR risk revealed that the early effect of antibiotic reduction was exhibited by the mitigation of maximum level of risky ARGs, prevalence of environmental AR pathogens, and HGT potential of ARGs mediated by phage structures. Overall, our findings provide insights into the antibiotic and ARG profiles in large-scale chicken farms with different rearing strategies and demonstrate a preliminary view of the performance of antibiotic reduction actions in China.},
}
@article {pmid39186711,
year = {2024},
author = {Smith, AM and Ramudzulu, M and Munk, P and Avot, BJP and Esterhuyse, KCM and van Blerk, N and Kwenda, S and Sekwadi, P},
title = {Metagenomics analysis of sewage for surveillance of antimicrobial resistance in South Africa.},
journal = {PloS one},
volume = {19},
number = {8},
pages = {e0309409},
pmid = {39186711},
issn = {1932-6203},
mesh = {South Africa ; *Sewage/microbiology ; *Metagenomics/methods ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Humans ; Wastewater/microbiology ; },
abstract = {Our 24-month study used metagenomics to investigate antimicrobial resistance (AMR) abundance in raw sewage from wastewater treatment works (WWTWs) in two municipalities in Gauteng Province, South Africa. At the AMR class level, data showed similar trends at all WWTWs, showing that aminoglycoside, beta-lactam, sulfonamide and tetracycline resistance was most abundant. AMR abundance differences were shown between municipalities, where Tshwane Metropolitan Municipality (TMM) WWTWs showed overall higher abundance of AMR compared to Ekurhuleni Metropolitan Municipality (EMM) WWTWs. Also, within each municipality, there were differing trends in AMR abundance. Notably, within TMM, certain AMR classes (macrolides and macrolides_streptogramin B) were in higher abundance at a WWTW serving an urban high-income area, while other AMR classes (aminoglycosides) were in higher abundance at a WWTW serving a semi-urban low income area. At the AMR gene level, all WWTWs samples showed the most abundance for the sul1 gene (encoding sulfonamide resistance). Following this, the next 14 most abundant genes encoded resistance to sulfonamides, aminoglycosides, macrolides, tetracyclines and beta-lactams. Notably, within TMM, some macrolide-encoding resistance genes (mefC, msrE, mphG and mphE) were in highest abundance at a WWTW serving an urban high-income area; while sul1, sul2 and tetC genes were in highest abundance at a WWTW serving a semi-urban low income area. Differential abundance analysis of AMR genes at WWTWs, following stratification of data by season, showed some notable variance in six AMR genes, of which blaKPC-2 and blaKPC-34 genes showed the highest prevalence of seasonal abundance differences when comparing data within a WWTW. The general trend was to see higher abundances of AMR genes in colder seasons, when comparing seasonal data within a WWTW. Our study investigated wastewater samples in only one province of South Africa, from WWTWs located within close proximity to one another. We would require a more widespread investigation at WWTWs distributed across all regions/provinces of South Africa, in order to describe a more comprehensive profile of AMR abundance across the country.},
}
@article {pmid39186442,
year = {2024},
author = {Chen, Y and Ma, W and Zhao, J and Stanton, C and Ross, RP and Zhang, H and Chen, W and Yang, B},
title = {Lactobacillus plantarum Ameliorates Colorectal Cancer by Ameliorating the Intestinal Barrier through the CLA-PPAR-γ Axis.},
journal = {Journal of agricultural and food chemistry},
volume = {72},
number = {36},
pages = {19766-19785},
doi = {10.1021/acs.jafc.4c02824},
pmid = {39186442},
issn = {1520-5118},
mesh = {*Lactobacillus plantarum/metabolism ; *PPAR gamma/metabolism/genetics ; Animals ; Mice ; *Colorectal Neoplasms/metabolism ; Humans ; *Probiotics/administration &amp; dosage/pharmacology ; Male ; *Linoleic Acids, Conjugated/pharmacology/metabolism ; *Mice, Inbred C57BL ; *Gastrointestinal Microbiome ; *Intestinal Mucosa/metabolism/microbiology ; Female ; NF-kappa B/metabolism/genetics ; Apoptosis/drug effects ; Claudin-1/metabolism/genetics ; Zonula Occludens-1 Protein/metabolism/genetics ; },
abstract = {Colorectal cancer (CRC) is the third-largest cancer worldwide. Lactobacillus can regulate the intestinal barrier and gut microbiota. However, the mechanisms of Lactobacillus that alleviate CRC remained unknown. This study aimed to explore the regulatory effect of Lactobacillus plantarum on CRC and its potential mechanism. CCFM8661 treatment significantly ameliorated CRC compared with phosphate-buffered solution (PBS) treatment in Apc[Min/+] mice. In addition, conjugated linoleic acid (CLA) was proved to be the key metabolite for CCFM8661 in ameliorating CRC by molecular biology techniques. Peroxisome proliferator-activated receptor γ (PPAR-γ) was proved to be the key receptor in ameliorating CRC by inhibitor intervention experiments. Moreover, supplementation with CCFM8661 ameliorated CRC by producing CLA to inhibit NF-κB pathway and pro-inflammatory cytokines, up-regulate ZO-1, Claudin-1, and MUC2, and promote tumor cell apoptosis in a PPAR-γ-dependent manner. Metagenomic analysis showed that CCFM8661 treatment significantly increased Odoribacter splanchnicus, which could ameliorate CRC by repairing the intestinal barrier. Clinical results showed that intestinal CLA, butyric acid, PPAR-γ, and Lactobacillus were significantly decreased in CRC patients, and these indicators were significantly negatively correlated with CRC. CCFM8661 alleviated CRC by ameliorating the intestinal barrier through the CLA-PPAR-γ axis. These results will promote the development of dietary probiotic supplements for CRC.},
}
@article {pmid39185682,
year = {2024},
author = {Maqsood, R and Holland, LA and Wu, LI and Begnel, ER and Adhiambo, J and Owiti, P and Chohan, BH and Gantt, S and Kinuthia, J and Wamalwa, D and Ojee, E and Richardson, BA and Slyker, J and Lehman, DA and Lim, ES},
title = {Gut virome and microbiome dynamics before and after SARS-CoV-2 infection in women living with HIV and their infants.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2394248},
pmid = {39185682},
issn = {1949-0984},
support = {R01 HD092311/HD/NICHD NIH HHS/United States ; },
mesh = {Humans ; Female ; *COVID-19/microbiology/virology ; *HIV Infections/microbiology/virology ; *Virome ; *Gastrointestinal Microbiome ; *SARS-CoV-2/genetics/isolation &amp; purification ; Adult ; Infant, Newborn ; *Feces/microbiology/virology ; Infant ; Bacteria/classification/isolation &amp; purification/genetics ; Longitudinal Studies ; },
abstract = {Microbiome perturbations can have long-term effects on health. The dynamics of the gut microbiome and virome in women living with HIV (WLHIV) and their newborn infants is poorly understood. Here, we performed metagenomic sequencing analyses on longitudinal stool samples including 23 mothers (13 WLHIV, 10 HIV-negative) and 12 infants that experienced SARS-CoV-2 infection with mild disease, as well as 40 mothers (18 WLHIV, 22 HIV-negative) and 60 infants that remained SARS-CoV-2 seronegative throughout the study follow-up. Regardless of HIV or SARS-CoV-2 status, maternal bacterial and viral profiles were distinct from infants. Using linear mixed effects models, we showed that the microbiome alpha diversity trajectory was not significantly different between SARS-CoV-2 seropositive and seronegative women. However, seropositive women's positive trajectory while uninfected was abruptly reversed after SARS-CoV-2 infection (p = 0.015). Gut virome signatures of women were not associated with SARS-CoV-2. Alterations in infant microbiome and virome diversities were generally not impacted by SARS-CoV-2 but were rather driven by development. We did not find statistically significant interactions between HIV and SARS-CoV-2 on the gut microbiome and virome. Overall, our study provides insights into the complex interplay between maternal and infant bacterial microbiome, virome, and the influence of SARS-CoV-2 and HIV status.},
}
@article {pmid39185240,
year = {2024},
author = {Laperriere, SM and Minch, B and Weissman, JL and Hou, S and Yeh, YC and Ignacio-Espinoza, JC and Ahlgren, NA and Moniruzzaman, M and Fuhrman, JA},
title = {Phylogenetic proximity drives temporal succession of marine giant viruses in a five-year metagenomic time-series.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39185240},
issn = {2692-8205},
support = {R01 GM120624/GM/NIGMS NIH HHS/United States ; },
abstract = {Nucleocytoplasmic Large DNA Viruses (NCLDVs, also called giant viruses) are widespread in marine systems and infect a broad range of microbial eukaryotes (protists). Recent biogeographic work has provided global snapshots of NCLDV diversity and community composition across the world's oceans, yet little information exists about the guiding 'rules' underpinning their community dynamics over time. We leveraged a five-year monthly metagenomic time-series to quantify the community composition of NCLDVs off the coast of Southern California and characterize these populations' temporal dynamics. NCLDVs were dominated by Algavirales (Phycodnaviruses, 59%) and Imitervirales (Mimiviruses, 36%). We identified clusters of NCLDVs with distinct classes of seasonal and non-seasonal temporal dynamics. Overall, NCLDV population abundances were often highly dynamic with a strong seasonal signal. The Imitervirales group had highest relative abundance in the more oligotrophic late summer and fall, while Algavirales did so in winter. Generally, closely related strains had similar temporal dynamics, suggesting that evolutionary history is a key driver of the temporal niche of marine NCLDVs. However, a few closely-related strains had drastically different seasonal dynamics, suggesting that while phylogenetic proximity often indicates ecological similarity, occasionally phenology can shift rapidly, possibly due to host-switching. Finally, we identified distinct functional content and possible host interactions of two major NCLDV orders-including connections of Imitervirales with primary producers like the diatom Chaetoceros and widespread marine grazers like Paraphysomonas and Spirotrichea ciliates. Together, our results reveal key insights on season-specific effect of phylogenetically distinct giant virus communities on marine protist metabolism, biogeochemical fluxes and carbon cycling.},
}
@article {pmid39185189,
year = {2024},
author = {Midani, FS and Danhof, HA and Mathew, N and Ardis, CK and Garey, KW and Spinler, JK and Britton, RA},
title = {Emerging Clostridioides difficile ribotypes have divergent metabolic phenotypes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39185189},
issn = {2692-8205},
support = {U01 AI124290/AI/NIAID NIH HHS/United States ; F32 AI136404/AI/NIAID NIH HHS/United States ; P30 CA125123/CA/NCI NIH HHS/United States ; R01 AI123278/AI/NIAID NIH HHS/United States ; U19 AI157981/AI/NIAID NIH HHS/United States ; T32 DK007664/DK/NIDDK NIH HHS/United States ; },
abstract = {UNLABELLED: Clostridioides difficile is a gram-positive spore-forming pathogen that commonly causes diarrheal infections in the developed world. Although C. difficile is a genetically diverse species, certain ribotypes are overrepresented in human infections. It is unknown if metabolic adaptations are essential for the emergence of these epidemic ribotypes. Here, we tested carbon substrate utilization by 88 C. difficile isolates and looked for differences in growth between 22 ribotypes. By profiling clinical isolates, we assert that C. difficile is a generalist species capable of growing on a variety of carbon substrates. Further, C. difficile strains clustered by phylogenetic relationship and displayed ribotype-specific and clade-specific metabolic capabilities. Surprisingly, we observed that two emerging lineages, ribotypes 023 and 255, have divergent metabolic phenotypes. In addition, although C. difficile Clade 5 is the most evolutionary distant clade and often detected in animals, it displayed more robust growth on simple dietary sugars than Clades 1-4. Altogether, our results corroborate the generalist metabolic strategy of C. difficile and demonstrate lineage-specific metabolic capabilities. In addition, our approach can be adapted to the study of additional pathogens to ascertain their metabolic niches in the gut.<br><br>IMPORTANCE: The gut pathogen Clostridioides difficile utilizes a wide range of carbon sources. Microbial communities can be rationally designed to combat C. difficile by depleting its preferred nutrients in the gut. However, C. difficile is genetically diverse with hundreds of identified ribotypes and most of its metabolic studies were performed with lab-adapted strains. Here, we profiled carbon metabolism by a myriad of C. difficile clinical isolates. While the metabolic capabilities of these isolates clustered by their genetic lineage, we observed surprising metabolic divergence between two emerging lineages. We also found that the most genetically distant clade grew robustly on simple dietary sugars, posing intriguing questions about the adaptation of C. difficile to the human gut. Altogether, our results underscore the importance of considering the metabolic diversity of pathogens in the study of their evolution and the rational design of therapeutic interventions.},
}
@article {pmid39185088,
year = {2024},
author = {Hu, L and Xu, Y and Li, J and Zhang, M and Sun, Z and Ban, Y and Tian, X and Liu, D and Hu, L},
title = {Gut microbiome characteristics of women with hypothyroidism during early pregnancy detected by 16S rRNA amplicon sequencing and shotgun metagenomic.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1369192},
pmid = {39185088},
issn = {2235-2988},
mesh = {Humans ; Female ; Pregnancy ; *Hypothyroidism/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; Adult ; *Dysbiosis/microbiology ; Bacteria/classification/genetics/isolation &amp; purification ; Pregnancy Complications/microbiology ; Metagenome ; Feces/microbiology ; },
abstract = {OBJECTIVE: This study aimed to explore the correlation between microbiota dysbiosis and hypothyroidism in early pregnancy by 16S rRNA amplicon sequencing combined with metagenomic sequencing.<br><br>METHODS: Sixty pregnant women (30 with hypothyroidism and 30 normal controls) were recruited for 16S rRNA amplicon sequencing, and 6 patients from each group were randomly selected for metagenomic sequencing to assess the gut microbiome profile.<br><br>RESULTS: The 16S rRNA results showed that beta-diversity in the hypothyroidism group was decreased. The relative abundances of the Prevotella and Paraprevotella genera increased in the hypothyroidism group, and Blautia predominated in the controls. The metagenomics results revealed that Prevotella_stercorea_CAG_629, Prevotella_hominis, Prevotella_sp_AM34_19LB, etc. were enriched in the hypothyroidism group at the species level. Functional analysis revealed that the pyridoxal 5'-phosphate synthase pdxT subunit module was decreased, and the short-chain fatty acid (SCFA) transporter and phospholipase/carboxylesterase modules were strongly enriched in the hypothyroidism group. Hypothyroidism patients had increased C-reactive protein (CRP), interleukin-2 (IL-2), IL-4, IL-10, and tumor necrosis factor (TNF)-&#x3b1; levels. The pyridoxal 5'-phosphate synthase pdxT subunit, the SCFA transporter, and the phospholipase/carboxylesterase module were associated with different Prevotella species.<br><br>CONCLUSION: In early pregnancy, women with hypothyroidism exhibit microbiota dysbiosis, and Prevotella may affect the metabolism of glutamate, SCFA, and phospholipases, which could be involved in the development of hypothyroidism during pregnancy.},
}
@article {pmid39185086,
year = {2024},
author = {Wang, X and Xiao, T and Lu, M and Wu, Z and Chen, L and Zhang, Z and Lu, W},
title = {Lower respiratory tract microbiome and lung cancer risk prediction in patients with diffuse lung parenchymal lesions.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1410681},
pmid = {39185086},
issn = {2235-2988},
mesh = {Humans ; *Lung Neoplasms/microbiology/pathology ; Male ; Female ; *Microbiota ; Middle Aged ; *Bronchoalveolar Lavage Fluid/microbiology ; Retrospective Studies ; Aged ; Lung/microbiology/pathology/diagnostic imaging ; High-Throughput Nucleotide Sequencing ; Adult ; Respiratory System/microbiology ; Metagenomics/methods ; Risk Factors ; },
abstract = {OBJECTIVE: In clinical practice, imaging manifestations of diffuse lung parenchymal lesions are common and indicative of various diseases, making differential diagnosis difficult. Some of these lesions are eventually diagnosed as lung cancer.<br><br>METHODS: Because respiratory microorganisms play an important role in lung cancer development, we searched for microbial markers that could predict the risk of lung cancer by retrospectively analyzing the lower respiratory tract (LRT) microbiome of 158 patients who were hospitalized in the First Affiliated Hospital of Guangzhou Medical University (March 2021-March 2023) with diffuse lung parenchymal lesions. The final diagnosis was lung cancer in 21 cases, lung infection in 93 cases, and other conditions (other than malignancy and infections) in 44 cases. The patient's clinical characteristics and the results of metagenomic next-generation sequencing of bronchoalveolar lavage fluid (BALF) were analyzed.<br><br>RESULTS: Body mass index (BMI) and LRT microbial diversity (Shannon, Simpson, species richness, and Choa1 index) were significantly lower (P< 0.001, respectively) and Lactobacillus acidophilus relative abundance in the LRT was significantly higher (P< 0.001) in patients with lung cancer. The relative abundance of L. acidophilus in BALF combined with BMI was a good predictor of lung cancer risk (area under the curve = 0.985, accuracy = 98.46%, sensitivity = 95.24%, and specificity = 100.00%; P< 0.001).<br><br>CONCLUSION: Our study showed that an imbalance in the component ratio of the microbial community, diminished microbial diversity, and the presence of specific microbial markers in the LRT predicted lung cancer risk in patients with imaging manifestations of diffuse lung parenchymal lesions.},
}
@article {pmid39184378,
year = {2024},
author = {Chung, HC and Friedberg, I and Bromberg, Y},
title = {Assembling bacterial puzzles: piecing together functions into microbial pathways.},
journal = {NAR genomics and bioinformatics},
volume = {6},
number = {3},
pages = {lqae109},
pmid = {39184378},
issn = {2631-9268},
abstract = {Functional metagenomics enables the study of unexplored bacterial diversity, gene families, and pathways essential to microbial communities. However, discovering biological insights with these data is impeded by the scarcity of quality annotations. Here, we use a co-occurrence-based analysis of predicted microbial protein functions to uncover pathways in genomic and metagenomic biological systems. Our approach, based on phylogenetic profiles, improves the identification of functional relationships, or participation in the same biochemical pathway, between enzymes over a comparable homology-based approach. We optimized the design of our profiles to identify potential pathways using minimal data, clustered functionally related enzyme pairs into multi-enzymatic pathways, and evaluated our predictions against reference pathways in the KEGG database. We then demonstrated a novel extension of this approach to predict inter-bacterial protein interactions amongst members of a marine microbiome. Most significantly, we show our method predicts emergent biochemical pathways between known and unknown functions. Thus, our work establishes a basis for identifying the potential functional capacities of the entire metagenome, capturing previously unknown and abstract functions into discrete putative pathways.},
}
@article {pmid39184367,
year = {2024},
author = {Frolov, AV and Vishnevskaya, MS and Viljanen, H and Montreuil, O and Akhmetova, LA},
title = {New data on trophic associations of dung beetles (Coleoptera, Scarabaeidae, Scarabaeinae) and lemurs (Primates, Lemuroidea) in Madagascar revealed by metabarcoding.},
journal = {Biodiversity data journal},
volume = {12},
number = {},
pages = {e130400},
pmid = {39184367},
issn = {1314-2828},
abstract = {Resource use and diet specialisation of Madagascan dung beetles have been little studied especially concerning the possible associations between specific dung beetle and lemur species. Pilot studies have demonstrated that amplicon sequencing is a promising tool for the lemur inventories. In the present contribution, we report the results of the gut content analysis of three endemic Madagascan dung beetles species: Helictopleurusclouei (Harold), Epilissusapotolamproides (Lebis) and Nanosdubitatus (Lebis). Amplicon metagenomics revealed trophic associations of these species with Eulemursanfordi (Archbold), Eu.fulvus (É.Geoffroy Saint-Hilaire) and Cheirogaleuscrossleyi (Grandidier), respectively. The reads of other mammal species, revealed by the analysis, including putative contaminations, are discussed.},
}
@article {pmid39184200,
year = {2024},
author = {Reynolds, G and Mumey, B and Strnadova-Neeley, V and Lachowiec, J},
title = {Hijacking a rapid and scalable metagenomic method reveals subgenome dynamics and evolution in polyploid plants.},
journal = {Applications in plant sciences},
volume = {12},
number = {4},
pages = {e11581},
pmid = {39184200},
issn = {2168-0450},
support = {P20 GM103474/GM/NIGMS NIH HHS/United States ; },
abstract = {PREMISE: The genomes of polyploid plants archive the evolutionary events leading to their present forms. However, plant polyploid genomes present numerous hurdles to the genome comparison algorithms for classification of polyploid types and exploring genome dynamics.<br><br>METHODS: Here, the problem of intra- and inter-genome comparison for examining polyploid genomes is reframed as a metagenomic problem, enabling the use of the rapid and scalable MinHashing approach. To determine how types of polyploidy are described by this metagenomic approach, plant genomes were examined from across the polyploid spectrum for both k-mer composition and frequency with a range of k-mer sizes. In this approach, no subgenome-specific k-mers are identified; rather, whole-chromosome k-mer subspaces were utilized.<br><br>RESULTS: Given chromosome-scale genome assemblies with sufficient subgenome-specific repetitive element content, literature-verified subgenomic and genomic evolutionary relationships were revealed, including distinguishing auto- from allopolyploidy and putative progenitor genome assignment. The sequences responsible were the rapidly evolving landscape of transposable elements. An investigation into the MinHashing parameters revealed that the downsampled k-mer space (genomic signatures) produced excellent approximations of sequence similarity. Furthermore, the clustering approach used for comparison of the genomic signatures is scrutinized to ensure applicability of the metagenomics-based method.<br><br>DISCUSSION: The easily implementable and highly computationally efficient MinHashing-based sequence comparison strategy enables comparative subgenomics and genomics for large and complex polyploid plant genomes. Such comparisons provide evidence for polyploidy-type subgenomic assignments. In cases where subgenome-specific repeat signal may not be adequate given a chromosomes' global k-mer profile, alternative methods that are more specific but more computationally complex outperform this approach.},
}
@article {pmid39184027,
year = {2024},
author = {Liu, Z and Qi, CJ and Shi, Y and Li, T and Fang, Y and Zhang, Q},
title = {Active herpesviruses are associated with intensive care unit (ICU) admission in patients pulmonary infection and alter the respiratory microbiome.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1441476},
pmid = {39184027},
issn = {1664-302X},
abstract = {BACKGROUND: The Herpesviridae family contains several human-related viruses, which are able to establish colonizing and latency in the human body, posing a significant threat to the prognosis of patients. Pulmonary infections represent one of the predominant infectious diseases globally, characterized by diverse and multifaceted clinical manifestations that have consistently attracted clinician's concern. However, the relationship of herpesviruses on the prognosis of pulmonary infections and the respiratory microbiota remains poorly understood.<br><br>METHODS: Here, we retrospectively analyzed respiratory samples from 100 patients with pulmonary infection detected by metagenomic next-generation sequencing (mNGS).<br><br>RESULTS: Employing mNGS, five herpesvirus species were detected: Human alphaherpesvirus 1 (HSV-1), Human gammaherpesvirus 4 (EBV), Human betaherpesvirus 5 (CMV), Human betaherpesvirus 7 (HHV-7), and Human betaherpesvirus 6B (HHV-6B). Regression analysis showed that the age and positivity of herpesviruses in patients were independently correlated with ICU admission rates. In addition, positivity of herpesvirus was related with increased ICU days and total hospital stay. The herpesvirus-positive group demonstrated markedly higher incidences of co-infections and fungi-positive, predominantly involving Pneumocystis jirovecii and Aspergillus fumigatus. Analysis of respiratory microbiota revealed a substantially altered community composition within the herpesvirus-positive group, and herpesviruses were significantly positively correlated with the diverse respiratory opportunistic pathogens.<br><br>CONCLUSION: Overall results substantiate that the active herpesviruses in patients with pulmonary infections were significantly associated with high ICU admission rate. Moreover, the herpesviruses promotes the dysbiosis of the respiratory microbiota and an increased proportion of co-infections. These insights could contribute to unraveling the underlying mechanisms connecting active herpesviruses to the progression of severe illnesses.},
}
@article {pmid39183848,
year = {2024},
author = {Bhuvaneshwar, K and Madhavan, S and Gusev, Y},
title = {Integrative genomic analysis of the lung tissue microenvironment in SARS-CoV-2 and NL63 patients.},
journal = {Heliyon},
volume = {10},
number = {12},
pages = {e32772},
pmid = {39183848},
issn = {2405-8440},
abstract = {The coronavirus disease 2019 (COVID-19) pandemic caused by the SARS-CoV-2 virus has affected over 700 million people, and caused over 7 million deaths throughout the world as of April 2024, and continues to affect people through seasonal waves. While over 675 million people have recovered from this disease globally, the lingering effects of the disease are still under study. Long term effects of SARS-CoV-2 infection, known as 'long COVID,' include a wide range of symptoms including fatigue, chest pain, cellular damage, along with a strong innate immune response characterized by inflammatory cytokine production. Three years after the pandemic, data about long covid studies are finally emerging. More clinical studies and clinical trials are needed to understand and determine the factors that predispose individuals to these long-term side effects. In this methodology paper, our goal was to apply data driven approaches in order to explore the multidimensional landscape of infected lung tissue microenvironment to better understand complex interactions between viral infection, immune response and the lung microbiome of patients with (a) SARS-CoV-2 virus and (b) NL63 coronavirus. The samples were analyzed with several machine learning tools allowing simultaneous detection and quantification of viral RNA amount at genome and gene level; human gene expression and fractions of major types of immune cells, as well as metagenomic analysis of bacterial and viral abundance. To contrast and compare specific viral response to SARS-COV-2, we analyzed deep sequencing data from additional cohort of patients infected with NL63 strain of corona virus. Our correlation analysis of three types of RNA-seq based measurements in patients i.e. fraction of viral RNA (at genome and gene level), Human RNA (transcripts and gene level) and bacterial RNA (metagenomic analysis), showed significant correlation between viral load as well as level of specific viral gene expression with the fractions of immune cells present in lung lavage as well as with abundance of major fractions of lung microbiome in COVID-19 patients. Our methodology-based proof-of-concept study has provided novel insights into complex regulatory signaling interactions and correlative patterns between the viral infection, inhibition of innate and adaptive immune response as well as microbiome landscape of the lung tissue. These initial findings could provide better understanding of the diverse dynamics of immune response and the side effects of the SARS-CoV-2 infection and demonstrates the possibilities of the various types of analyses that could be performed from this type of data.},
}
@article {pmid39183814,
year = {2024},
author = {Li, GX and Gopchandani, K and Brazer, N and Tippett, A and Choi, C and Hsiao, HM and Oseguera, M and Foresythe, A and Bhattacharya, S and Servellita, V and Sotomayor Gonzalez, A and Spinler, JK and Gonzalez, MD and Gulick, D and Kraft, C and Kasinathan, V and Wang, YFW and Dien Bard, J and Chen, PY and Flores-Vazquez, J and Odom John, AR and Planet, PJ and Devaraj, S and Annapragada, AV and Luna, RA and Chiu, CY and Rostad, CA},
title = {Clinical Features and Outcomes of Pediatric and Adult Patients Hospitalized for Coronavirus Disease 2019: A Comparison Across Age Strata.},
journal = {Open forum infectious diseases},
volume = {11},
number = {8},
pages = {ofae443},
pmid = {39183814},
issn = {2328-8957},
support = {R61 HD105618/HD/NICHD NIH HHS/United States ; },
abstract = {BACKGROUND: Coronavirus disease 2019 (COVID-19) continues to cause hospitalizations and severe disease in children and adults.<br><br>METHODS: This study compared the risk factors, symptoms, and outcomes of children and adults hospitalized for COVID-19 from March 2020 to May 2023 across age strata at 5 US sites participating in the Predicting Viral-Associated Inflammatory Disease Severity in Children with Laboratory Diagnostics and Artificial Intelligence consortium. Eligible patients had an upper respiratory swab that tested positive for severe acute respiratory syndrome coronavirus 2 by nucleic acid amplification. Adjusted odds ratios (aOR) of clinical outcomes were determined for children versus adults, for pediatric age strata compared to adolescents (12-17 years), and for adult age strata compared to young adults (22-49 years).<br><br>RESULTS: Of 9101 patients in the Predicting Viral-Associated Inflammatory Disease Severity in Children with Laboratory Diagnostics and Artificial Intelligence cohort, 1560 were hospitalized for COVID-19 as the primary reason. Compared to adults (22-105 years, n = 675), children (0-21 years, n = 885) were less commonly vaccinated (14.3% vs 34.5%), more commonly infected with the Omicron variant (49.5% vs 26.1%) and had fewer comorbidities (P < .001 for most comparisons), except for lung disease (P = .24). After adjusting for confounding variables, children had significantly lower odds of receiving supplemental oxygen (aOR, 0.57; 95% confidence interval, .35-.92) and death (aOR, 0.011; 95% confidence interval, <.01-.58) compa--red to adults. Among pediatric age strata, adolescents 12-17 years had the highest odds of receiving supplemental oxygen, high-flow oxygen, and ICU admission. Among adults, those 50-64 years had the highest odds of mechanical ventilation and ICU admission.<br><br>CONCLUSIONS: Clinical outcomes of COVID-19 differed across pediatric and adult age strata. Adolescents experienced the most severe disease among children, whereas adults 50-64 years experienced the most severe disease among adults.},
}
@article {pmid39182818,
year = {2024},
author = {Fang, C and Liu, KD and Tian, FJ and Li, JY and Li, SJ and Zhang, RM and Sun, J and Fang, LX and Ren, H and Wang, MG and Liao, XP},
title = {Metagenomic analysis unveiled the response of microbial community and antimicrobial resistome in natural water body to duck farm sewage.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {361},
number = {},
pages = {124784},
doi = {10.1016/j.envpol.2024.124784},
pmid = {39182818},
issn = {1873-6424},
abstract = {Sewages from duck farms are often recognized as a major source of antimicrobial resistance and pathogenic bacteria discharged to natural water bodies, but few studies depicted the dynamic changes in resistome and microbial communities in the rivers under immense exposure of sewage discharge. In this study, we investigated the ecological and environmental risks of duck sewages to the rivers that geographically near to the duck farms with short-distance (<1 km) using 16S rRNA amplicon and metagenomic sequencing. The results showed that a total of 20 ARG types were identified with abundances ranged from 0.61 to 1.33 cpc. Of note, the genes modulate resistances against aminoglycoside, bacitracin and beta-lactam were the most abundant ARGs. Limnohabitans, Fluviibacter and Cyanobium were the top 3 predominant genera in the microbial community. The alpha diversity of overall microbial community decrease while the abundance of pathogen increase during the input of sewage within 200 m. Sul1 and bacA were the dominant ARGs brought from duck farm sewage. The community variations of ARGs and microbiome were primarily driven by pH and temperature. Total phosphorus was significantly correlated to alpha diversity and top 30 ARGs subtype. Stochastic processes was the dominated microbial assembly pattern and did not be altered by sewage. We also highlighted the ecological risk caused by blaGES which possibly could be mitigated by Cyanobacteria, and the natural water body can purify partial ARGs as well as microbiome from duck farms sewage. These findings expanded our knowledge regarding the ecological risks by wastes from the livestock farm, and underscoring the necessity to monitor ARGs in farm-surrounding water bodies.},
}
@article {pmid39182795,
year = {2024},
author = {Wang, SP and Sun, ZY and Wang, ST and Tang, YQ},
title = {Microbial mechanisms of biochar addition on carbon and nitrogen synergistic retention during distilled grain waste composting: Insights from metagenomic analysis.},
journal = {Bioresource technology},
volume = {411},
number = {},
pages = {131346},
doi = {10.1016/j.biortech.2024.131346},
pmid = {39182795},
issn = {1873-2976},
mesh = {*Nitrogen ; *Carbon/pharmacology ; *Charcoal/chemistry/pharmacology ; *Composting/methods ; Metagenomics/methods ; Edible Grain/metabolism ; Soil Microbiology ; Soil/chemistry ; },
abstract = {To elucidate the mechanism of biochar addition on carbon and nitrogen retention during distilled grain (DGW) composting, this study investigated the losses of carbon and nitrogen and functional genes related to carbon and nitrogen metabolisms between biochar-treated and control composts. The addition of biochar significantly increased carbon and nitrogen retention by 13.5% and 33.8%, respectively. The difference in core carbon metabolism genes indicated that biochar addition inhibited CO2 release and promoted carbon fixation during the later composting phase, leading to improved carbon retention. Nitrogen metabolism analysis indicated that biochar addition suppressed early-phase ammoniation and late-phase denitrification and promoted nitrification and ammonia assimilation during the later stages of composting, thereby preserving nitrogen. During the later composting phase, biochar addition enhanced carbon-nitrogen coupling metabolism activity, leading to the synchronous retention of carbon and nitrogen. These findings elucidate the mechanism of biochar addition on carbon and nitrogen retention during DGW composting.},
}
@article {pmid39182764,
year = {2024},
author = {Zhao, Y and Tan, J and Fang, L and Jiang, L},
title = {Harnessing meta-omics to unveil and mitigate methane emissions in ruminants: Integrative approaches and future directions.},
journal = {The Science of the total environment},
volume = {951},
number = {},
pages = {175732},
doi = {10.1016/j.scitotenv.2024.175732},
pmid = {39182764},
issn = {1879-1026},
mesh = {*Methane/metabolism ; Animals ; *Ruminants ; Metabolomics ; Metagenomics ; Air Pollutants/analysis ; Greenhouse Gases ; Rumen/metabolism ; Gastrointestinal Microbiome ; Genomics ; },
abstract = {Methane emissions from enteric fermentation present a dual challenge globally: they not only contribute significantly to atmospheric greenhouse gases but also represent a considerable energy loss for ruminant animals. Utilizing high-throughput omics technologies to analyze rumen microbiome samples (meta-omics, i.e., metagenomics, metatranscriptomics, metaproteomics, metabolomics) holds vast potential for uncovering the intricate interplay between diet, microbiota, and methane emissions in these animals. The primary obstacle is the effective integration of diverse meta-omic approaches and their broader application across different ruminant species. Genetic variability significantly impacts methane production in ruminants, suggesting that genomic selection could be a viable strategy to reduce emissions. While substantial research has been conducted on the microbiological aspects of methane production, there remains a critical need to delineate the specific genetic interactions between the host and its microbiome. Advancements in meta-omics technologies are poised to shed light on these interactions, enhancing our understanding of the genetic factors that govern methane output. This review explores the potential of meta-omics to accelerate genetic advancements that could lead to reduced methane emissions in ruminants. By employing a systems biology approach, the integration of various omics technologies allows for the identification of key genomic regions and genetic markers linked to methane production. These markers can then be leveraged in selective breeding programs to cultivate traits associated with lower emissions. Moreover, the review addresses current challenges in applying genomic selection for this purpose and discusses how omics technologies can overcome these obstacles. The systematic integration and analysis of diverse biological data provide deeper insights into the genetic underpinnings and overall biology of methane production traits in ruminants. Ultimately, this comprehensive approach not only aids in reducing the environmental impact of agriculture but also contributes to the sustainability and efficiency of livestock management.},
}
@article {pmid39182301,
year = {2024},
author = {Peruzzo, A and Petrin, S and Boscolo Anzoletti, A and Mancin, M and Di Cesare, A and Sabatino, R and Lavagnolo, MC and Beggio, G and Baggio, G and Danesi, P and Barco, L and Losasso, C},
title = {The integration of omics and cultivation-dependent methods could effectively determine the biological risks associated with the utilization of soil conditioners in agriculture.},
journal = {Journal of hazardous materials},
volume = {478},
number = {},
pages = {135567},
doi = {10.1016/j.jhazmat.2024.135567},
pmid = {39182301},
issn = {1873-3336},
mesh = {*Agriculture ; *Soil Microbiology ; *Sewage/microbiology ; *Bacteria/genetics ; Soil/chemistry ; Composting ; Metagenomics ; Fertilizers ; },
abstract = {In the circular economy, reusing agricultural residues, treated biowaste, and sewage sludges-commonly referred to as soil conditioners-in agriculture is essential for converting waste into valuable resources. However, these materials can also contribute to the spread of antimicrobial-resistant pathogens in treated soils. In this study, we analyzed different soil conditioners categorized into five groups: compost from source-separated biowaste and green waste, agro-industrial digestate, digestate from anaerobic digestion of source-separated biowaste, compost from biowaste digestate, and sludges from wastewater treatment plants. Under Italian law, only the first two categories are approved for agricultural use, despite Regulation 1009/2019/EU allowing the use of digestate from anaerobic digestion of source-separated biowaste in CE-marked fertilizers. We examined the bacterial community and associated resistome of each sample using metagenomic approaches. Additionally, we detected and isolated various pathogens to provide a comprehensive understanding of the potential risks associated with sludge application in agriculture. The compost samples exhibited higher bacterial diversity and a greater abundance of potentially pathogenic bacteria compared to other samples, except for wastewater treatment plant sludges, which had the highest frequency of Salmonella isolation and resistome diversity. Our findings suggest integrating omics and cultivation-dependent methods to accurately assess the biological risks of using sludge in agriculture.},
}
@article {pmid39182227,
year = {2024},
author = {Chilton, PM and Ghare, SS and Charpentier, BT and Myers, SA and Rao, AV and Petrosino, JF and Hoffman, KL and Greenwell, JC and Tyagi, N and Behera, J and Wang, Y and Sloan, LJ and Zhang, J and Shields, CB and Cooper, GE and Gobejishvili, L and Whittemore, SR and McClain, CJ and Barve, SS},
title = {Age-associated temporal decline in butyrate-producing bacteria plays a key pathogenic role in the onset and progression of neuropathology and memory deficits in 3×Tg-AD mice.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2389319},
pmid = {39182227},
issn = {1949-0984},
support = {P20 GM113226/GM/NIGMS NIH HHS/United States ; R01 AG061065/AG/NIA NIH HHS/United States ; U01 AA022618/AA/NIAAA NIH HHS/United States ; P50 AA024337/AA/NIAAA NIH HHS/United States ; U01 AA026936/AA/NIAAA NIH HHS/United States ; I01 CX002219/CX/CSRD VA/United States ; },
mesh = {Animals ; *Butyrates/metabolism ; *Gastrointestinal Microbiome ; Mice ; *Alzheimer Disease/microbiology/pathology/metabolism ; *Memory Disorders/microbiology/metabolism/pathology ; *Bacteria/classification/metabolism/genetics/isolation &amp; purification ; *Disease Models, Animal ; *Dysbiosis/microbiology ; Hippocampus/metabolism/pathology ; Mice, Transgenic ; Male ; Disease Progression ; Brain-Gut Axis/physiology ; Brain/metabolism/pathology ; },
abstract = {Alterations in the gut-microbiome-brain axis are increasingly being recognized to be involved in Alzheimer's disease (AD) pathogenesis. However, the functional consequences of enteric dysbiosis linking gut microbiota and brain pathology in AD progression remain largely undetermined. The present work investigated the causal role of age-associated temporal decline in butyrate-producing bacteria and butyrate in the etiopathogenesis of AD. Longitudinal metagenomics, neuropathological, and memory analyses were performed in the 3×Tg-AD mouse model. Metataxonomic analyses showed a significant temporal decline in the alpha diversity marked by a decrease in butyrate-producing bacterial communities and a concurrent reduction in cecal butyrate production. Inferred metagenomics analysis identified the bacterial acetyl-CoA pathway as the main butyrate synthesis pathway impacted. Concomitantly, there was an age-associated decline in the transcriptionally permissive acetylation of histone 3 at lysines 9 and 14 (H3K9/K14-Ac) in hippocampal neurons. Importantly, these microbiome-gut-brain changes preceded AD-related neuropathology, including oxidative stress, tau hyperphosphorylation, memory deficits, and neuromuscular dysfunction, which manifest by 17-18 months. Initiation of oral administration of tributyrin, a butyrate prodrug, at 6 months of age mitigated the age-related decline in butyrate-producing bacteria, protected the H3K9/K14-Ac status, and attenuated the development of neuropathological and cognitive changes associated with AD pathogenesis. These data causally implicate age-associated decline in butyrate-producing bacteria as a key pathogenic feature of the microbiome-gut-brain axis affecting the onset and progression of AD. Importantly, the regulation of butyrate-producing bacteria and consequent butyrate synthesis could be a significant therapeutic strategy in the prevention and treatment of AD.},
}
@article {pmid39182147,
year = {2024},
author = {Ji, R and Wan, J and Liu, J and Zheng, J and Xiao, T and Pan, Y and Lin, W},
title = {Linking morphology, genome, and metabolic activity of uncultured magnetotactic Nitrospirota at the single-cell level.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {158},
pmid = {39182147},
issn = {2049-2618},
support = {42388101//National Natural Science Foundation of China/ ; T2225011//National Natural Science Foundation of China/ ; YSBR-097//CAS Project for Young Scientists in Basic Research/ ; },
mesh = {*Genome, Bacterial ; *Phylogeny ; *Single-Cell Analysis ; Bacteria/metabolism/classification/genetics ; Magnetosomes/metabolism/genetics ; Lakes/microbiology ; Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: Magnetotactic bacteria (MTB) are a unique group of microorganisms that sense and navigate through the geomagnetic field by biomineralizing magnetic nanoparticles. MTB from the phylum Nitrospirota (previously known as Nitrospirae) thrive in diverse aquatic ecosystems. They are of great interest due to their production of hundreds of magnetite (Fe3O4) magnetosome nanoparticles per cell, which far exceeds that of other MTB. The morphological, phylogenetic, and genomic diversity of Nitrospirota MTB have been extensively studied. However, the metabolism and ecophysiology of Nitrospirota MTB are largely unknown due to the lack of cultivation techniques.<br><br>METHODS: Here, we established a method to link the morphological, genomic, and metabolic investigations of an uncultured Nitrospirota MTB population (named LHC-1) at the single-cell level using nanoscale secondary-ion mass spectrometry (NanoSIMS) in combination with rRNA-based in situ hybridization and target-specific mini-metagenomics.<br><br>RESULTS: We magnetically separated LHC-1 from a freshwater lake and reconstructed the draft genome of LHC-1 using genome-resolved mini-metagenomics. We found that 10 LHC-1 cells were sufficient as a template to obtain a high-quality draft genome. Genomic analysis revealed that LHC-1 has the potential for CO2 fixation and NO3[-] reduction, which was further characterized at the single-cell level by combining stable-isotope incubations and NanoSIMS analyses over time. Additionally, the NanoSIMS results revealed specific element distributions in LHC-1, and that the heterogeneity of CO2 and NO3[-] metabolisms among different LHC-1 cells increased with incubation time.<br><br>CONCLUSIONS: To our knowledge, this study provides the first metabolic measurements of individual Nitrospirota MTB cells to decipher their ecophysiological traits. The procedure constructed in this study provides a promising strategy to simultaneously investigate the morphology, genome, and ecophysiology of uncultured microbes in natural environments. Video Abstract.},
}
@article {pmid39182035,
year = {2024},
author = {Velázquez-Fernández, JB and Aceves Suriano, CE and Thalasso, F and Montoya-Ciriaco, N and Dendooven, L},
title = {Structural and functional bacterial biodiversity in a copper, zinc and nickel amended bioreactor: shotgun metagenomic study.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {313},
pmid = {39182035},
issn = {1471-2180},
mesh = {*Bioreactors/microbiology ; *Zinc/metabolism ; *Nickel/metabolism ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; *Metagenomics ; *Copper/metabolism ; *Biodiversity ; Wastewater/microbiology/chemistry ; },
abstract = {BACKGROUND: At lower concentrations copper (Cu), zinc (Zn) and nickel (Ni) are trace metals essential for some bacterial enzymes. At higher concentrations they might alter and inhibit microbial functioning in a bioreactor treating wastewater. We investigated the effect of incremental concentrations of Cu, Zn and Ni on the bacterial community structure and their metabolic functions by shotgun metagenomics. Metal concentrations reported in previous studies to inhibit bacterial metabolism were investigated.<br><br>RESULTS: At 31.5&#xa0;&#x3bc;M Cu, 112.4&#xa0;&#x3bc;M Ni and 122.3&#xa0;&#x3bc;M Zn, the most abundant bacteria were Achromobacter and Agrobacterium. When the metal concentration increased 2 or fivefold their abundance decreased and members of Delftia, Stenotrophomonas and Sphingomonas dominated. Although the heterotrophic metabolic functions based on the gene profile was not affected when the metal concentration increased, changes in the sulfur biogeochemical cycle were detected. Despite the large variations in the bacterial community structure when concentrations of Cu, Zn and Ni increased in the bioreactor, functional changes in carbon metabolism were small.<br><br>CONCLUSIONS: Community richness and diversity replacement indexes decreased significantly with increased metal concentration. Delftia antagonized Pseudomonas and members of Xanthomonadaceae. The relative abundance of most bacterial genes remained unchanged despite a five-fold increase in the metal concentration, but that of some EPS genes required for exopolysaccharide synthesis, and those related to the reduction of nitrite to nitrous oxide decreased which may alter the bioreactor functioning.},
}
@article {pmid39181512,
year = {2024},
author = {Li, Y and Barati, B and Li, J and Verhoestraete, E and Rousseau, DPL and Van Hulle, SWH},
title = {Lab-scale evaluation of Microalgal-Bacterial granular sludge as a sustainable alternative for brewery wastewater treatment.},
journal = {Bioresource technology},
volume = {411},
number = {},
pages = {131331},
doi = {10.1016/j.biortech.2024.131331},
pmid = {39181512},
issn = {1873-2976},
mesh = {*Microalgae/metabolism ; *Sewage/microbiology ; *Wastewater/chemistry ; *Nitrogen ; *Bacteria/metabolism ; Biological Oxygen Demand Analysis ; Water Purification/methods ; Phosphorus ; Carbon/pharmacology ; Waste Disposal, Fluid/methods ; Beer ; Phosphates ; Bioreactors ; },
abstract = {Microalgal-bacterial granular sludge (MBGS) could offer a sustainable alternative to traditional aerobic methods in brewery wastewater (BWW) treatment. This study compared MBGS with conventional activated sludge (AS) in treating real BWW and highlighted its advantages and challenges. MBGS achieved comparable chemical oxygen demand removal efficiency (93%) compared to AS (89%). Additionally, MBGS exhibited higher phosphate removal capabilities than AS. Extra nitrogen was added to influent to balance C/N ratio of BWW. MBGS was robust in handling C/N ratio fluctuations with an 82% total nitrogen removal efficiency. Metagenomic analysis further indicated that most of the genes involved in carbon, nitrogen and phosphorus metabolism were up-regulated in MBGS compared to AS. Despite changes in the microbial community and settling ability due to high starch and sugar content in BWW, MBGS demonstrated high efficiency and sustainability. Further research should optimize MBGS operation strategies to fully realize its potential for sustainable BWW treatment.},
}
@article {pmid39181304,
year = {2024},
author = {Yu, Y and Ai, T and Huang, J and Jin, L and Yu, X and Zhu, X and Sun, J and Zhu, L},
title = {Metabolism of isodecyl diphenyl phosphate in rice and microbiome system: Differential metabolic pathways and underlying mechanisms.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {361},
number = {},
pages = {124803},
doi = {10.1016/j.envpol.2024.124803},
pmid = {39181304},
issn = {1873-6424},
abstract = {Isodecyl diphenyl phosphate (IDDP) is among the emerging aromatic organophosphate esters (aryl-OPEs) that pose risks to both human beings and other organisms. This study aims to investigate the translocation and biotransformation behavior of IDDP in rice and the rhizosphere microbiome through hydroponic exposure (the duration of hydroponic exposure was 10 days). The rhizosphere microbiome 9-FY was found to efficiently eliminate IDDP, thereby reducing its uptake in rice tissues and mitigating the negative impact of IDDP on rice growth. Furthermore, this study proposed the first-ever transformation pathways of IDDP, identifying hydrolysis, hydroxylation, methylation, methoxylation, carboxylation, and glucuronidation products. Notably, the methylation and glycosylation pathways were exclusively observed in rice, indicating that the transformation of IDDP in rice may be more complex than in microbiome 9-FY. Additionally, the presence of the product COOH-IDDP in rice suggested that there might be an exchange of degradation products between rice and rhizobacteria, implying their potential interaction. This finding highlights the significance of rhizobacteria's role which cannot be overlooked in the accumulation and transformation of organic pollutants in grain crops. The study revealed active members in 9-FY during IDDP degradation, and metagenomic analysis indicated that most of the active populations contained IDDP-degrading genes. Moreover, transcriptome sequencing showed that cytochrome P450, acid phosphatase, glucosyltransferase, and methyltransferases genes in rice were up-regulated, which was further confirmed by RT-qPCR. This provides insight into the intermediate products identified in rice, such as hydrolysis, hydroxylated, glycosylated, and methylated products. These results significantly contribute to our understanding of the translocation and transformation of organophosphate esters (OPEs) in plants and the rhizosphere microbiome, and reveal the fate of OPEs in rice and microbiome system to ensure the paddy yield and rice safety.},
}
@article {pmid39181265,
year = {2024},
author = {Dong, W and Zhou, J and Zhang, CJ and Yang, Q and Li, M},
title = {Methylotrophic substrates stimulated higher methane production than competitive substrates in mangrove sediments.},
journal = {The Science of the total environment},
volume = {951},
number = {},
pages = {175677},
doi = {10.1016/j.scitotenv.2024.175677},
pmid = {39181265},
issn = {1879-1026},
mesh = {*Methane/metabolism ; *Geologic Sediments/microbiology ; *Wetlands ; China ; Microbiota ; Bacteria/metabolism/classification ; },
abstract = {Although mangrove forests can uptake atmospheric CO2 and store carbon as organic matter called "blue carbon", it is also an important natural source of greenhouse gas methane. Methanogens are major contributors to methane and play important roles in the global carbon cycle. However, our understanding of the key microbes and metabolic pathways responsible for methanogenesis under specific substrates in mangrove sediments is still very limited. Here, we set an anaerobic incubation to evaluate the responses of methanogens in mangrove sediments from South China to the addition of diverse methanogenic substrates (H2/CO2, acetate, trimethylamine (TMA), and methanethiol (MT)) and further investigated the dynamics of the whole microbial community. Our results showed that diverse substrates stimulated methanogenic activities at different times. The stimulation of methanogenesis was more pronounced at early and late periods by the addition of methylotrophic substrates TMA and MT, respectively. The amplicon sequencing analysis showed that genus Methanococcoides was mainly responsible for TMA-utilized methanogenesis in mangrove sediment, while the multitrophic Methanococcus was most abundant in H2/CO2 and MT treatments. Apart from that, the bacteria enrichments of Syntrophotalea, Clostridium_sensu_stricto_12, Fusibacter in MT treatments might also be associated with the stimulation of methane production. In addition, the metagenomic analysis suggested that Methanosarcinaceae was also one of the key methanogens in MT treatments with different genomic information compared to that in TMA treatments. Finally, the total relative abundances of methanogenesis-related genes were also highest in TMA and MT treatments. These results will help advance our understanding of the contributions of different methanogenesis pathways and methanogens to methane emissions in mangrove sediments.},
}
@article {pmid39181210,
year = {2024},
author = {Zhang, YH and Xie, R and Dai, CS and Gao, HW and Zhou, G and Qi, TT and Wang, WY and Wang, H and Cui, YM},
title = {Thyroid hormone receptor-beta agonist HSK31679 alleviates MASLD by modulating gut microbial sphingolipids.},
journal = {Journal of hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jhep.2024.08.008},
pmid = {39181210},
issn = {1600-0641},
abstract = {BACKGROUND &amp; AIMS: As the first approved medication for metabolic dysfunction-associated steatohepatitis (MASH), thyroid hormone receptor-beta (THR-β) agonist MGL-3196 (Resmetirom) is highly spotlighted as the liver-directed, bioactive oral drug. However, it was also identified with remarkable heterogeneity of individual clinical efficacy and its interference with gut microbiota in host hepatoenteral circulation was still undocumented.<br><br>METHODS: We compared MASH attenuation by MGL-3196 and its derivative drug HSK31679 between germ-free (GF) and specific-pathogen free (SPF) mice to evaluate the role of gut microbiota. Then cross-omics analyses of microbial metagenome, metabolome and single-cell RNA-sequencing were applied into the randomized, double-blind, placebo-controlled multiple-ascending-dose (MAD) cohort of HSK31679 treatment (n = 40), to comprehensively investigate the altered gut microbiota metabolism and circulating immune signatures.<br><br>RESULTS: HSK31679 outperformed MGL-3196 in ameliorating MASH diet-induced steatohepatitis of SPF mice but not GF mice. In the MAD cohort of HSK31679, relative abundance of B. thetaiotaomicron was significantly enriched to impair glucosylceramide synthase (GCS)-catalyzed monoglucosylation of microbial Cer(d18:1/16:0) and Cer(d18:1/24:1). In stark contrast to the non-inferiority MASH resolution between MGL-3196 and HSK31679 for GF[BT&#x394;GCS] mice, HSK31679 manifested superior steatohepatitis alleviation than MGL-3196 for GF[BTWT] mice, due to its steric hindrance with R123 and Y401 of gut microbial GCS. For participants with high fecal GCS activity, the administration of 160 mg HSK31679 induced a shift in peripheral compartments towards an immunosuppressive niche, characterized by decreased CD8&#x3b1;[+] dendritic cells and MINCLE[+] macrophages.<br><br>CONCLUSIONS: This study provided novel insights into the indispensable gut microbiota for HSK31679 treatment, which revealed microbial GCS may serve as its prognostic biomarker of MASH treatment, as well as the new target for further strategies of microbiota-based MASH therapeutics.<br><br>IMPACT AND IMPLICATIONS: Remarkable heterogeneity of individual clinical efficacy of THR-&#x3b2; agonists and their interferences with microbiome in host hepatoenteral circulation are poorly understood. In our current germ-free mice models and randomized, double-blind multiple-dose cohort study, we identified microbial GCS as the prognostic biomarker of HSK31679 treatment, as well as the new target for further strategies of microbiota-based MASLD therapeutics.},
}
@article {pmid39181078,
year = {2024},
author = {Wei, Q and Yin, Y and Tong, Q and Gong, Z and Shi, Y},
title = {Multi-omics analysis of excessive nitrogen fertilizer application: Assessing environmental damage and solutions in potato farming.},
journal = {Ecotoxicology and environmental safety},
volume = {284},
number = {},
pages = {116916},
doi = {10.1016/j.ecoenv.2024.116916},
pmid = {39181078},
issn = {1090-2414},
abstract = {Potatoes (Solanum tuberosum L.) are the third largest food crop globally and are pivotal for global food security. Widespread N fertilizer waste in potato cultivation has caused diverse environmental issues. This study employed microbial metagenomic sequencing to analyze the causes behind the declining N use efficiency (NUE) and escalating greenhouse gas emissions resulting from excessive N fertilizer application. Addressing N fertilizer inefficiency through breeding has emerged as a viable solution for mitigating overuse in potato cultivation. In this study, transcriptome and metabolome analyses were applied to identify N fertilizer-responsive genes. Metagenomic sequencing revealed that excessive N fertilizer application triggered alterations in the population dynamics of 11 major bacterial phyla, consequently affecting soil microbial functions, particularly N metabolism pathways and bacterial secretion systems. Notably, the enzyme levels associated with NO3[-] increased, and those associated with NO and N2O increased. Furthermore, excessive N fertilizer application enhanced soil virulence factors and increased potato susceptibility to diseases. Transcriptome and metabolome sequencing revealed significant impacts of excessive N fertilizer use on lipid and amino acid metabolism pathways. Weighted gene co‑expression network analysis (WGCNA) was adopted to identify two genes associated with N fertilizer response: PGSC0003DMG400021157 and PGSC0003DMG400009544.},
}
@article {pmid39180955,
year = {2024},
author = {Li, Y and Yang, B and Kong, Y and Tao, Y and Zhao, Z and Li, Y and Zhang, Y},
title = {Correlation between intracellular electron transfer and gene expression for electrically conductive pili in electroactive bacteria during anaerobic digestion with ethanol.},
journal = {Water research},
volume = {265},
number = {},
pages = {122307},
doi = {10.1016/j.watres.2024.122307},
pmid = {39180955},
issn = {1879-2448},
mesh = {Electron Transport ; *Ethanol/metabolism ; Anaerobiosis ; Electric Conductivity ; Fimbriae, Bacterial/metabolism ; Bacteria/metabolism ; Gene Expression ; },
abstract = {Ethanol feeding has been widely documented as an economical and effective strategy for establishing direct interspecies electron transfer (DIET) during anaerobic digestion. However, the mechanisms involved are still unclear, especially on correlation between intracellular electron transfer in electroactive bacteria and their gene expression for electrically conductive pili (e-pili), the most essential electrical connection component for DIET. Upon cooling from room temperature, the conductivity of digester aggregates with ethanol exponentially increased by an order of magnitude (from 45.5 to 125.4 μS/cm), whereas which with its metabolites (acetaldehyde [from 40.5 to 54.4 μS/cm] or acetate [from 32.1 to 50.4 μS/cm]) did not increase significantly. In addition, the digester aggregates only with ethanol were observed with a strong dependence of conductivity on pH. Metagenomic and metatranscriptomic analysis showed that Desulfovibrio desulfuricans was the most dominant and metabolically active bacterium that contained and highly expressed the genes for e-pili. Abundance of genes encoding the total type IV pilus assembly proteins (6.72E-04 vs 1.24E-03, P < 0.05), PilA that determined the conductive properties (2.22E-04 vs 2.44E-04, P > 0.05), and PilB that proceeded the polymerization of pilin (1.56E-04 vs 3.52E-03, P < 0.05) with ethanol was lower than that with acetaldehyde. However, transcript abundance of these genes with ethanol was generally higher than that with acetaldehyde. In comparison to acetaldehyde, ethanol increased the transcript abundance of genes encoding the key enzymes involved in NADH/NAD[+] transformation on complex I and ATP synthesis on complex V in intracellular electron transport chain. The improvement of intracellular electron transfer in D. desulfuricans suggested that electrons were intracellularly energized with high energy to activate e-pili during DIET.},
}
@article {pmid39180787,
year = {2024},
author = {Seara-Morais, GJ and Miraglia, FFO and Hidal, JT and Camargo, LFA and Mangueira, CLP and Doi, AM and Amgarten, DE and Dorlass, EG and Santana, RAF and Pinho, JRR},
title = {Identification of a Orthohantavirus strain by clinical metagenomics in Brazil.},
journal = {Diagnostic microbiology and infectious disease},
volume = {110},
number = {4},
pages = {116501},
doi = {10.1016/j.diagmicrobio.2024.116501},
pmid = {39180787},
issn = {1879-0070},
abstract = {We describe a case of a 33-year-old male presented with fever, myalgia, nausea, and asthenia for six days. The patient lived in a rural area. Initial hypotheses included arbovirus infection, viral hepatitis, and Lyme disease. Reverse transcriptase polymerase chain reaction (RT-PCR) tests for Dengue, Zika, and Chikungunya resulted negative. We were able to recover complete S, L, and M segments of virus in the Orthohantavirus genome.},
}
@article {pmid39180723,
year = {2024},
author = {Jiang, L and Hao, Y and Han, D and Dong, W and Yang, A and Sun, Z and Ge, Y and Duan, S and Zhang, X and Dai, Z},
title = {Gut microbiota dysbiosis deteriorates immunoregulatory effects of tryptophan via colonic indole and LBP/HTR2B-mediated macrophage function.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae166},
pmid = {39180723},
issn = {1751-7370},
abstract = {Tryptophan (Trp) has been shown to regulate immune function by modulating gut serotonin (5-HT) metabolism and signaling. However, the mechanisms underlying the microbial modulation of gut 5-HT signaling in gut inflammation with gut microbiota dysbiosis require further investigation. Here, we investigated the effects of Trp supplementation on the composition and metabolism of the gut microbiome and 5-HT signaling-related gut immune function using a dextran sodium sulfate (DSS)-induced colitis mouse model coupled with antibiotic exposure. The results showed that antibiotic treatment before but not during DSS treatment decreased the immunoregulatory effects of Trp and aggravated gut inflammation and body weight loss in mice. Metagenomic analysis revealed that the fecal microbiota transplantation (FMT) of Trp-enriched gut microbiota to recipient mice subject to antibiotic preexposure and DSS treatment aggravated inflammation by increasing the relative abundances of Lactobacillus and Parabacteroides and the microbial production of indole coupled with the activation of the 5-HT receptor HTR2B in the colon. Transcriptomic analysis showed that HTR2B agonist administration strengthened the beneficial effects of Trp in DSS-induced colitis mice with antibiotic exposure by reducing gut lipopolysaccharide-binding protein (LBP) production, IκB-α/nuclear factor-κB signaling, and M1 macrophage polarization. Indole treatment reduced LBP production and M1 macrophage polarization both in mice with DSS-induced colitis and in lipopolysaccharide-treated mouse macrophages; however, the HTR2B antagonist reversed the effects of indole. Our findings provide the basis for developing new dietary and therapeutic interventions to improve gut microbiota dysbiosis-associated inflammatory gut disorders and diseases.},
}
@article {pmid39180208,
year = {2024},
author = {Wang, YC and Jiang, TM and Mo, L and Lu, HZ and Quan, LH and Zhong, P and Guan, Y},
title = {Distribution of Antibiotic-Resistant Genes in Intestines of Infants and Influencing Factors.},
journal = {Critical reviews in eukaryotic gene expression},
volume = {34},
number = {8},
pages = {59-73},
pmid = {39180208},
issn = {1045-4403},
mesh = {Humans ; Female ; *Feces/microbiology ; *Anti-Bacterial Agents/pharmacology ; *Milk, Human/microbiology ; Infant ; Infant, Newborn ; Intestines/microbiology ; Male ; Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; Gastrointestinal Microbiome/genetics/drug effects ; Bacteria/genetics/drug effects ; Drug Resistance, Microbial/genetics ; },
abstract = {The objective of this study is to assess the prevalence of antibiotic-resistant genes (ARGs) in the intestines of infants and the factors affecting their distribution. Breast milk and infant stool samples were collected from nine full-term, healthy mother-infant pairs. The bacterial distribution and various types of ARGs present in the samples were analyzed using metagenomic next-generation sequencing. Over a period spanning from 2 to 240 d after birth, a total of 273 types of ARGs were identified in both infant feces and breast milk, exhibiting a trend of increasing prevalence over time. High concentrations of representative ARG populations were identified in the intestines of infants, especially at 12-15 d after birth. These populations included APH3-Ib, tetW/N/W, mphA, and Haemophilus influenzae PBP3, and multiple ARG Escherichia coli soxS that were resistant to common clinically used aminoglycoside, tetracycline, macrolide, and beta-lactam antibiotics. Gammaproteobacteria and Bacilli, especially Enterococcus, Staphylococcus, Acinetobacter, Streptococcus, and Escherichia were among the identified ARG carriers. Maternal age and body mass index (present and before pregnancy), infant sex, maternal consumption of probiotic yogurt during pregnancy, and lactation might be substantial factors influencing the occurrence of ARG-carrying bacteria and ARG distribution in the infant feces. These results indicate that environmental factors may influence the distribution of ARG-carrying bacteria and ARGs themselves in infants during early life. Providing appropriate recommendations regarding maternal age, body mass index during pregnancy, and use of probiotic products could potentially mitigate the transmission of antibiotic-resistant microbiota and ARGs, thereby diminishing the risk of antibiotic-resistant infections and safeguarding children's health.},
}
@article {pmid39180123,
year = {2024},
author = {Horigan, S and Kettenburg, G and Kistler, A and Ranaivoson, HC and Andrianiaina, A and Andry, S and Raharinosy, V and Randriambolamanantsoa, TH and Tato, CM and Lacoste, V and Heraud, JM and Dussart, P and Brook, CE},
title = {Detection, characterization, and phylogenetic analysis of novel astroviruses from endemic Malagasy fruit bats.},
journal = {Virology journal},
volume = {21},
number = {1},
pages = {195},
pmid = {39180123},
issn = {1743-422X},
support = {1R01A|129822-01/NH/NIH HHS/United States ; GCE/ID OPP1211841//Bill and Melinda Gates Foundation/ ; PREEMPT Program Cooperative Agreement no D18AC00031//Defense Sciences Office, DARPA/ ; },
mesh = {Animals ; *Chiroptera/virology ; *Phylogeny ; *Astroviridae/genetics/isolation &amp; purification/classification ; *Astroviridae Infections/veterinary/virology/epidemiology ; *Metagenomics ; High-Throughput Nucleotide Sequencing ; Madagascar ; Genome, Viral/genetics ; Sequence Analysis, DNA ; },
abstract = {Bats (order: Chiroptera) are known to host a diverse range of viruses, some of which present a human public health risk. Thorough viral surveillance is therefore essential to predict and potentially mitigate zoonotic spillover. Astroviruses (family: Astroviridae) are an understudied group of viruses with a growing amount of indirect evidence for zoonotic transfer. Astroviruses have been detected in bats with significant prevalence and diversity, suggesting that bats may act as important astrovirus hosts. Most astrovirus surveillance in wild bat hosts has, to date, been restricted to single-gene PCR detection and concomitant Sanger sequencing; additionally, many bat species and many geographic regions have not yet been surveyed for astroviruses at all. Here, we use metagenomic Next Generation Sequencing (mNGS) to detect astroviruses in three species of Madagascar fruit bats, Eidolon dupreanum, Pteropus rufus, and Rousettus madagascariensis. We detect numerous partial sequences from all three species and one near-full length astrovirus sequence from Rousettus madagascariensis, which we use to characterize the evolutionary history of astroviruses both within bats and the broader mammalian clade, Mamastrovirus. Taken together, applications of mNGS implicate bats as important astrovirus hosts and demonstrate novel patterns of bat astrovirus evolutionary history, particularly in the Southwest Indian Ocean region.},
}
@article {pmid39180058,
year = {2024},
author = {Hua, X and McGoldrick, J and Nakrour, N and Staller, K and Chung, DC and Xavier, RJ and Khalili, H},
title = {Gut microbiome structure and function in asymptomatic diverticulosis.},
journal = {Genome medicine},
volume = {16},
number = {1},
pages = {105},
pmid = {39180058},
issn = {1756-994X},
support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; R01 AG068390/AG/NIA NIH HHS/United States ; DK043351//Center for the study of inflammatory bowel disease/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; Aged ; Metagenomics/methods ; Colonoscopy ; Metagenome ; Bacteria/classification/genetics ; },
abstract = {BACKGROUND: Colonic diverticulosis, the most common lesion found in routine colonoscopy, affects more than 50% of individuals aged ≥ 60 years. Emerging evidence suggest that dysbiosis of gut microbiota may play an important role in the pathophysiology of diverticular disease. However, specific changes in microbial species and metabolic functions in asymptomatic diverticulosis remain unknown.<br><br>METHODS: In a cohort of US adults undergoing screening colonoscopy, we analyzed the gut microbiota using shotgun metagenomic sequencing. Demographic factors, lifestyle, and medication use were assessed using a baseline questionnaire administered prior to colonoscopy. Taxonomic structures and metabolic pathway abundances were determined using MetaPhlAn3 and HUMAnN3. We used multivariate association with linear models to identify microbial species and metabolic pathways that were significantly different between asymptomatic diverticulosis and controls, while adjusting for confounders selected a priori including age at colonoscopy, sex, body mass index (BMI), and dietary pattern.<br><br>RESULTS: Among 684 individuals undergoing a screening colonoscopy, 284 (42%) had diverticulosis. Gut microbiome composition explained 1.9% variation in the disease status of asymptomatic diverticulosis. We observed no significant differences in the overall diversity of gut microbiome between asymptomatic diverticulosis and controls. However, microbial species Bifidobacterium pseudocatenulatum and Prevotella copri were significantly enriched in controls (q value&#x2009;=&#x2009;0.19 and 0.14, respectively), whereas Roseburia intestinalis, Dorea sp. CAG:317, and Clostridium sp. CAG: 299 were more abundant in those with diverticulosis (q values&#x2009;=&#x2009;0.17, 0.24, and 0.10, respectively). We observed that the relationship between BMI and diverticulosis appeared to be limited to carriers of Bifidobacterium pseudocatenulatum and Roseburia intestinalis (Pinteraction&#x2009;=&#x2009;0.09).<br><br>CONCLUSIONS: Our study provides the first large-scale evidence supporting taxonomic and functional shifts of the gut microbiome in individuals with asymptomatic diverticulosis. The suggestive interaction between gut microbiota and BMI on prevalent diverticulosis deserves future investigations.},
}
@article {pmid39179660,
year = {2024},
author = {Wang, S and Sun, S and Wang, Q and Chen, H and Guo, Y and Cai, M and Yin, Y and Ma, S and Wang, H},
title = {PathoTracker: an online analytical metagenomic platform for Klebsiella pneumoniae feature identification and outbreak alerting.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {1038},
pmid = {39179660},
issn = {2399-3642},
support = {32141001//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81991533//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Klebsiella pneumoniae/genetics/isolation &amp; purification ; *Metagenomics/methods ; Humans ; *Disease Outbreaks ; *Klebsiella Infections/microbiology/epidemiology/diagnosis ; *Phylogeny ; China/epidemiology ; Nanopore Sequencing/methods ; Databases, Genetic ; Genome, Bacterial ; },
abstract = {Clinical metagenomics (CMg) Nanopore sequencing can facilitate infectious disease diagnosis. In China, sub-lineages ST11-KL64 and ST11-KL47 Carbapenem-resistant Klebsiella pneumoniae (CRKP) are widely prevalent. We propose PathoTracker, a specially compiled database and arranged method for strain feature identification in CMg samples and CRKP traceability. A database targeting high-prevalence horizontal gene transfer in CRKP strains and a ST11-only database for distinguishing two sub-lineages in China were created. To make the database user-friendly, facilitate immediate downstream strain feature identification from raw Nanopore metagenomic data, and avoid the need for phylogenetic analysis from scratch, we developed data analysis methods. The methods included pre-performed phylogenetic analysis, gene-isolate-cluster index and multilevel pan-genome database and reduced storage space by 10-fold and random-access memory by 52-fold compared with normal methods. PathoTracker can provide accurate and fast strain-level analysis for CMg data after 1 h Nanopore sequencing, allowing early warning of outbreaks. A user-friendly page (http://PathoTracker.pku.edu.cn/) was developed to facilitate online analysis, including strain-level feature, species identifications and phylogenetic analyses. PathoTracker proposed in this study will aid in the downstream analysis of CMg.},
}
@article {pmid39179206,
year = {2024},
author = {Barone Lumaga, R and Tagliamonte, S and De Rosa, T and Valentino, V and Ercolini, D and Vitaglione, P},
title = {Consumption of a Sourdough-Leavened Croissant Enriched with a Blend of Fibers Influences Fasting Blood Glucose in a Randomized Controlled Trial in Healthy Subjects.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tjnut.2024.08.015},
pmid = {39179206},
issn = {1541-6100},
abstract = {BACKGROUND: An incorrect lifestyle, including diet, is responsible for the worldwide dramatic increase in obesity and type 2 diabetes. Increasing dietary fiber consumption may lead to health benefits, and reformulation of bakery products may be a strategy to globally improve the diet.<br><br>OBJECTIVES: This study aimed to assess the impact of a 2-wk breakfast consumption with a sourdough-leavened croissant containing a blend of dietary fiber from 10 sources (4.8 g/100 g, croissant enriched with dietary fibers [FIBCRO]), compared with a control croissant (dietary fibers 1.3 g/100 g, CONCRO) on daily energy intake, appetite, metabolic variables, and the gut microbiome.<br><br>METHODS: Thirty-two healthy participants were randomly allocated to 2 groups consuming FIBCRO or CONCRO. Participants self-recorded their diet and appetite through 7-d weighted food diaries and visual analog scales every day over the 2 wk. At baseline and after the intervention, fasting blood and urine samples, and fecal samples were collected beside blood pressure, anthropometry, and body composition. Serum glucose, lipids, C-reactive protein, and insulin according to the official methods and serum dipeptidyl peptidase-4 (DPPIV) activity by photometric method were measured. Polyphenols and urolithins in urines were analyzed by Liquid chromatography-tandem mass spectrometry (LC/MS/MS), whereas gut microbiome in feces by shotgun metagenomics.<br><br>RESULTS: FIBCRO consumption improved fasting blood glucose compared with CONCRO (mean changes from baseline -2.0 mg/dL in FIBCRO compared with +3.1 mg/dL in CONCRO, P = 0.022), also reducing serum DPPIV activity by 1.7 IU/L (P = 0.01) and increasing urinary excretion of urolithin A-sulfate by 6.9 ng/mg creatinine (P = 0.04) compared with baseline. No further changes in any of the monitored variables or in the gut microbiome were detected.<br><br>CONCLUSIONS: Results suggested that a 2-wk consumption of a sourdough croissant claimed as "source of dietary fiber" improved fasting glycemia compared with a conventional sourdough croissant in healthy subjects. The reduced serum DPPIV activity and increased bioavailability of urolithin likely contributed to determine that effect independently from gut microbiome changes. This trial was registered at clinicaltrials.gov as NCT04999280.},
}
@article {pmid39179139,
year = {2024},
author = {Gao, N and Zhuang, Y and Zheng, Y and Li, Y and Wang, Y and Zhu, S and Fan, M and Tian, W and Jiang, Y and Wang, Y and Cui, M and Suo, C and Zhang, T and Jin, L and Chen, X and Xu, K},
title = {Investigating the link between gut microbiome and bone mineral density: The role of genetic factors.},
journal = {Bone},
volume = {188},
number = {},
pages = {117239},
doi = {10.1016/j.bone.2024.117239},
pmid = {39179139},
issn = {1873-2763},
mesh = {Humans ; *Bone Density/genetics ; Female ; *Gastrointestinal Microbiome/genetics ; Male ; Middle Aged ; Aged ; *Osteoporosis/genetics/microbiology ; Feces/microbiology ; },
abstract = {Osteoporosis is a complex metabolic bone disease that severely undermines the quality of life and overall health of the elderly. While previous studies have established a close relationship between gut microbiome and host bone metabolism, the role of genetic factors has received less scrutiny. This research aims to identify potential taxa associated with various bone mineral density states, incorporating assessments of genetic factors. Fecal microbiome profiles from 605 individuals (334 females and 271 males) aged 55-65 from the Taizhou Imaging Study with osteopenia (n = 270, 170 women) or osteoporosis (n = 94, 85 women) or normal (n = 241, 79 women) were determined using shotgun metagenomic sequencing. The linear discriminant analysis was employed to identify differentially enriched taxa. Utilizing the Kyoto Encyclopedia of Genes and Genomes for annotation, functional pathway analysis was conducted to identify differentially metabolic pathways. Polygenic risk score for osteoporosis was estimated to represent genetic susceptibility to osteoporosis, followed by stratification and interaction analyses. Gut flora diversity did not show significant differences among various bone mineral groups. After multivariable adjustment, certain species, such as Clostridium leptum, Fusicatenibacter saccharivorans and Roseburia hominis, were enriched in osteoporosis patients. Statistically significant interactions between the polygenic risk score and taxa Roseburia faecis, Megasphaera elsdenii were observed (P for interaction = 0.005, 0.018, respectively). Stratified analyses revealed a significantly negative association between Roseburia faecis and bone mineral density in the low-genetic-risk group (β = -0.045, P < 0.05), while Turicimonas muris was positively associated with bone mineral density in the high-genetic-risk group (β = 4.177, P < 0.05) after multivariable adjustments. Functional predictions of the gut microbiome indicated an increase in pathways related to structural proteins in high-genetic-risk patients, while low-genetic-risk patients exhibited enrichment in enzyme-related pathways. This study emphasizes the association between gut microbes and bone mass, offering new insights into the interaction between genetic background and gut microbiome.},
}
@article {pmid39179065,
year = {2024},
author = {Abedanzadeh, S and Ariaeenejad, S and Karimi, B and Moosavi-Movahedi, AA},
title = {Revolutionizing protein hydrolysis in wastewater: Innovative immobilization of metagenome-derived protease in periodic mesoporous organosilica with imidazolium framework.},
journal = {International journal of biological macromolecules},
volume = {278},
number = {Pt 4},
pages = {134966},
doi = {10.1016/j.ijbiomac.2024.134966},
pmid = {39179065},
issn = {1879-0003},
mesh = {*Enzymes, Immobilized/chemistry/metabolism ; *Wastewater/chemistry ; *Metagenome ; Porosity ; Hydrolysis ; Peptide Hydrolases/chemistry/metabolism ; Enzyme Stability ; Imidazoles/chemistry ; Adsorption ; Organosilicon Compounds/chemistry ; Metal-Organic Frameworks/chemistry ; },
abstract = {This research focused on utilizing periodic mesoporous organosilica with imidazolium framework (PMO-IL), to immobilize a metagenome-sourced protease (PersiProtease1), thereby enhancing its functional efficiency and catalytic effectiveness in processing primary proteins found in tannery wastewater. The successful immobilization of enzyme was confirmed through the use of N2 adsorption-desorption experiment, XRD, FTIR, TEM, FESEM, EDS and elemental analytical techniques. The immobilized enzyme exhibited greater stability in the presence of various metal ions and inhibitors compared to its free form. Furthermore, enzyme binding to PMO-IL nanoparticles (NPs) reduced leaching, evidenced by only 11.41 % of enzyme leakage following a 120-min incubation at 80 °C and 6.99 % after 240 min at 25 °C. Additionally, PersiPro@PMO-IL maintained impressive operational consistency, preserving 62.24 % of its activity over 20 cycles. It also demonstrated notable stability under saline conditions, with an increase of 1.5 times compared to the free enzyme in the presence of 5 M NaCl. The rate of collagen hydrolysis by the immobilized protease was 46.82 % after a 15-minute incubation at 60 °C and marginally decreased to 39.02 % after 20 cycles indicative of sustained efficacy without significant leaching throughout the cycles. These findings underscore the effectiveness of PMO-IL NPs as a viable candidate for treating wastewater containing protein.},
}
@article {pmid39178987,
year = {2024},
author = {Shukla, V and Singh, S and Verma, S and Verma, S and Rizvi, AA and Abbas, M},
title = {Targeting the microbiome to improve human health with the approach of personalized medicine: Latest aspects and current updates.},
journal = {Clinical nutrition ESPEN},
volume = {63},
number = {},
pages = {813-820},
doi = {10.1016/j.clnesp.2024.08.005},
pmid = {39178987},
issn = {2405-4577},
abstract = {The intricate ecosystem of microorganisms residing within and on the human body, collectively known as the microbiome, significantly influences human health. Imbalances in this microbiome, referred to as dysbiosis, have been associated with various diseases, prompting the exploration of novel therapeutic approaches. Personalized medicine, Tailors treatments to individual patient characteristics, offers a promising avenue for addressing microbiome-related health issues. This review highlights recent developments in utilizing personalized medicine to target the microbiome, aiming to enhance health outcomes. Noteworthy strategies include fecal microbiota transplantation (FMT), where healthy donor microbes are transferred to patients, showing promise in treating conditions such as recurrent Clostridium difficile infection. Additionally, probiotics, which are live microorganisms similar to beneficial gut inhabitants, and prebiotics, non-digestible compounds promoting microbial growth, are emerging as tools to restore microbiome balance. The integration of these approaches, known as synbiotics, enhances microbial colonization and therapeutic effects. Advances in metagenomics and sequencing technologies provide the means to understand individual microbiome profiles, enabling tailored interventions. This paper aims to present the latest insights in leveraging personalized medicine to address microbiome-related health concerns, envisioning a future where microbiome-based therapies reshape disease management and promote human health.},
}
@article {pmid39178591,
year = {2024},
author = {Gao, FZ and Hu, LX and Liu, YS and Qiao, LK and Chen, ZY and Su, JQ and He, LY and Bai, H and Zhu, YG and Ying, GG},
title = {Unveiling the overlooked small-sized microbiome in river ecosystems.},
journal = {Water research},
volume = {265},
number = {},
pages = {122302},
doi = {10.1016/j.watres.2024.122302},
pmid = {39178591},
issn = {1879-2448},
mesh = {*Rivers/microbiology ; *Microbiota ; *Ecosystem ; Metagenomics ; Bacteria/genetics ; },
abstract = {Enriching microorganisms using a 0.22-μm pore size is a general pretreatment procedure in river microbiome research. However, it remains unclear the extent to which this method loses microbiome information. Here, we conducted a comparative metagenomics-based study on microbiomes with sizes over 0.22 μm (large-sized) and between 0.22 μm and 0.1 μm (small-sized) in a subtropical river. Although the absolute concentration of small-sized microbiome was about two orders of magnitude lower than that of large-sized microbiome, sequencing only large-sized microbiome resulted in a significant loss of microbiome diversity. Specifically, the microbial community was different between two sizes, and 347 genera were only detected in small-sized microbiome. Small-sized microbiome had much more diverse viral community than large-sized fraction. The viruses had abundant ecological functions and were hosted by 825 species of 169 families, including pathogen-related families. Small-sized microbiome had distinct antimicrobial resistance risks from large-sized microbiome, showing an enrichment of eight antibiotic resistance gene (ARG) types as well as the detection of 140 unique ARG subtypes and five enriched risk rank I ARGs. Draft genomes of five major resistant pathogens having diverse ecological and pollutant-degrading functions were only assembled in small-sized microbiome. These findings provide novel insights into river ecosystems, and highlight the overlooked small-sized microbiome in the environment.},
}
@article {pmid39178299,
year = {2024},
author = {Han, X and Zhang, L and Zhang, M and Xin, Q and Zhao, Y and Wen, Y and Deng, H and Zhu, J and Dai, Q and Han, M and Yang, T and Lahu, S and Jiang, F and Chen, Z},
title = {Amugulang virus, a novel hantavirus harboured by small rodents in Hulunbuir, China.},
journal = {Emerging microbes &amp; infections},
volume = {13},
number = {1},
pages = {2396893},
pmid = {39178299},
issn = {2222-1751},
mesh = {Animals ; China ; *Orthohantavirus/genetics/classification/isolation &amp; purification ; *Phylogeny ; *Rodentia/virology ; Humans ; Hantavirus Infections/virology/veterinary/epidemiology ; Genome, Viral ; Metagenomics ; Hemorrhagic Fever with Renal Syndrome/virology/veterinary/epidemiology ; },
abstract = {The Hulunbuir region, known for its diverse terrain and rich wildlife, is a hotspot for various natural epidemic diseases. Between 2021 and 2023, we collected 885 wild rodent samples from this area, representing three families, seven genera, and eleven species. Metagenomic analysis identified three complete nucleic acid sequences from the S, M, and L segments of the Hantaviridae family, which were closely related to the Khabarovsk virus. The nucleotide coding sequences for S, M, and L (1392 nt, 3465 nt, and 6491 nt, respectively) exhibited similarities of 82.34%, 81.68%, and 81.94% to known sequences, respectively, while protein-level analysis indicated higher similarities of 94.92%, 94.41%, and 95.87%, respectively. Phylogenetic analysis placed these sequences within the same clade as the Khabarovsk, Puumala, Muju, Hokkaido, Topografov, and Tatenalense viruses, all of which are known to cause febrile diseases in humans. Immunofluorescence detection of nucleic acid-positive rodent kidney samples using sera from patients with hemorrhagic fever and renal syndrome confirmed the presence of viral particles. Based on these findings, we propose that this virus represents a new member of the Hantaviridae family, tentatively named the Amugulang virus, after its primary distribution area.},
}
@article {pmid39178288,
year = {2024},
author = {Buscaglia, M and Iriarte, JL and Schulz, F and Díez, B},
title = {Adaptation strategies of giant viruses to low-temperature marine ecosystems.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae162},
pmid = {39178288},
issn = {1751-7370},
abstract = {Microbes in marine ecosystems have evolved their gene content to thrive successfully in the cold. Although this process has been reasonably well studied in bacteria and selected eukaryotes, less is known about the impact of cold environments on the genomes of viruses that infect eukaryotes. Here, we analyzed cold adaptations in giant viruses (Nucleocytoviricota and Mirusviricota) from austral marine environments and compared them with their Arctic and temperate counterparts. We recovered giant virus metagenome-assembled genomes (98 Nucleocytoviricota and 12 Mirusviricota MAGs) from 61 newly sequenced metagenomes and metaviromes from sub-Antarctic Patagonian fjords and Antarctic seawater samples. When analyzing our data set alongside Antarctic and Arctic giant viruses MAGs already deposited in the Global Ocean Eukaryotic Viral (GOEV) database, we found that Antarctic and Arctic giant viruses predominantly inhabit sub-10°C environments, featuring a high proportion of unique phylotypes in each ecosystem. In contrast, giant viruses in Patagonian fjords were subject to broader temperature ranges and showed a lower degree of endemicity. However, despite differences in their distribution, giant viruses inhabiting low-temperature marine ecosystems evolved genomic cold-adaptation strategies that led to changes in genetic functions and amino acid frequencies that ultimately affect both gene content and protein structure. Such changes seem to be absent in their mesophilic counterparts. The uniqueness of these cold-adapted marine giant viruses may now be threatened by climate change, leading to a potential reduction in their biodiversity.},
}
@article {pmid39178040,
year = {2024},
author = {Liu, L and Feng, T and Liu, Q and Liao, M and Liu, B and Li, M},
title = {Characterization of the vaginal microbiota in infertile women with repeated implantation failure.},
journal = {Acta microbiologica et immunologica Hungarica},
volume = {71},
number = {3},
pages = {263-271},
doi = {10.1556/030.2024.02323},
pmid = {39178040},
issn = {1588-2640},
mesh = {Humans ; Female ; *Vagina/microbiology ; Adult ; *Infertility, Female/microbiology ; *Microbiota ; *Bacteria/classification/isolation &amp; purification/genetics ; Embryo Implantation ; Pregnancy ; Fertilization in Vitro ; },
abstract = {Although the relationship between vaginal microorganisms and fertility has been well established, only few studies have investigated vaginal microorganisms in women undergoing in vitro fertilization (IVF). Our aim was to study the differences in vaginal microbiota between infertile women with repeated implantation failure (RIF) and those who achieved clinical pregnancy in their first frozen embryo transfer cycle. We compared the vaginal microbiota of patients with a history of RIF (n = 37) with that of the control group (n = 43). Following DNA extraction, metagenomic sequencing was employed for the analysis of alpha and beta diversities, distinctions in bacterial species, and the functional annotation of microbial genes. Furthermore, disparities between the two groups were revealed. Alpha diversity analysis revealed that the Shannon index was higher in the RIF group (P < 0.05). There were differences in the beta diversity between groups (P = 0.16). At the bacterial family level, the relative abundance of Actinomycetaceae (P = 0.013) and Ruminococcaceae (P = 0.013) were significantly higher in the RIF group. At the genus level, the abundances of Actinomyces (P = 0.028) and Subdoligranulum (P = 0.013) were significantly higher in the RIF group. At the species level, the abundances of Prevotella timonensis (P = 0.028), Lactobacillus jensenii (P = 0.049), and Subdoligranulum (P = 0.013) were significantly higher in the RIF group. Significant differences in family, genus, species, alpha and beta diversity were observed in the vaginal microbiota between groups. Notably, among these findings, the Subdoligranulum genus emerged as the most prominent correlating factor.},
}
@article {pmid39177328,
year = {2024},
author = {Howe, KL and Zaugg, J and Mason, OU},
title = {Novel, active, and uncultured hydrocarbon-degrading microbes in the ocean.},
journal = {Applied and environmental microbiology},
volume = {90},
number = {9},
pages = {e0122424},
pmid = {39177328},
issn = {1098-5336},
support = {DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; RFP-VI: Research Grants [Consortium for Simulation of Oil-Microbial Interactions in the Ocean (CSOMIO)]//Gulf of Mexico Research Initiative (GoMRI)/ ; },
mesh = {*Hydrocarbons/metabolism ; *Seawater/microbiology ; *Biodegradation, Environmental ; *Bacteria/metabolism/classification/genetics/isolation &amp; purification ; Oceans and Seas ; Metagenome ; Metagenomics ; Petroleum Pollution ; Phylogeny ; },
abstract = {Given the vast quantity of oil and gas input to the marine environment annually, hydrocarbon degradation by marine microorganisms is an essential ecosystem service. Linkages between taxonomy and hydrocarbon degradation capabilities are largely based on cultivation studies, leaving a knowledge gap regarding the intrinsic ability of uncultured marine microbes to degrade hydrocarbons. To address this knowledge gap, metagenomic sequence data from the Deepwater Horizon (DWH) oil spill deep-sea plume was assembled to which metagenomic and metatranscriptomic reads were mapped. Assembly and binning produced new DWH metagenome-assembled genomes that were evaluated along with their close relatives, all of which are from the marine environment (38 total). These analyses revealed globally distributed hydrocarbon-degrading microbes with clade-specific substrate degradation potentials that have not been reported previously. For example, methane oxidation capabilities were identified in all Cycloclasticus. Furthermore, all Bermanella encoded and expressed genes for non-gaseous n-alkane degradation; however, DWH Bermanella encoded alkane hydroxylase, not alkane 1-monooxygenase. All but one previously unrecognized DWH plume member in the SAR324 and UBA11654 have the capacity for aromatic hydrocarbon degradation. In contrast, Colwellia were diverse in the hydrocarbon substrates they could degrade. All clades encoded nutrient acquisition strategies and response to cold temperatures, while sensory and acquisition capabilities were clade specific. These novel insights regarding hydrocarbon degradation by uncultured planktonic microbes provides missing data, allowing for better prediction of the fate of oil and gas when hydrocarbons are input to the ocean, leading to a greater understanding of the ecological consequences to the marine environment.IMPORTANCEMicrobial degradation of hydrocarbons is a critically important process promoting ecosystem health, yet much of what is known about this process is based on physiological experiments with a few hydrocarbon substrates and cultured microbes. Thus, the ability to degrade the diversity of hydrocarbons that comprise oil and gas by microbes in the environment, particularly in the ocean, is not well characterized. Therefore, this study aimed to utilize non-cultivation-based 'omics data to explore novel genomes of uncultured marine microbes involved in degradation of oil and gas. Analyses of newly assembled metagenomic data and previously existing genomes from other marine data sets, with metagenomic and metatranscriptomic read recruitment, revealed globally distributed hydrocarbon-degrading marine microbes with clade-specific substrate degradation potentials that have not been previously reported. This new understanding of oil and gas degradation by uncultured marine microbes suggested that the global ocean harbors a diversity of hydrocarbon-degrading bacteria, which can act as primary agents regulating ecosystem health.},
}
@article {pmid39177227,
year = {2024},
author = {Deng, Y and Nong, Z and Wei, M and Xu, Y and Luo, Y and Li, X and Zhao, R and Yang, Z and Pan, L},
title = {Characteristics and function of the gut microbiota in patients with IgA nephropathy via metagenomic sequencing technology.},
journal = {Renal failure},
volume = {46},
number = {2},
pages = {2393754},
pmid = {39177227},
issn = {1525-6049},
mesh = {Humans ; *Glomerulonephritis, IGA/microbiology ; *Gastrointestinal Microbiome/genetics ; Male ; Female ; Adult ; *Feces/microbiology ; *Metagenomics/methods ; Case-Control Studies ; Middle Aged ; Moraxella/isolation &amp; purification/genetics ; Escherichia coli/isolation &amp; purification/genetics ; Acinetobacter/isolation &amp; purification/genetics ; Metagenome ; Young Adult ; },
abstract = {OBJECTIVE: The aim of this study was to investigate the characteristics and related functional pathways of the gut microbiota in patients with IgA nephropathy (IgAN) through metagenomic sequencing technology.<br><br>METHODS: We enrolled individuals with primary IgAN, including patients with normal and abnormal renal function. Additionally, we recruited healthy volunteers as the healthy control group. Stool samples were collected, and species and functional annotation were performed through fecal metagenome sequencing. We employed linear discriminant analysis effect size (LEfSe) analysis to identify significantly different bacterial microbiota and functional pathways. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis was used to annotate microbiota functions, and redundancy analysis (RDA) was performed to analyze the factors affecting the composition and distribution of the gut microbiota.<br><br>RESULTS: LEfSe analysis revealed differences in the gut microbiota between IgAN patients and healthy controls. The characteristic microorganisms in the IgAN group were classified as Escherichia coli, with a significantly greater abundance than that in the healthy control group (p&#x2009;<&#x2009;0.05). The characteristic microorganisms in the IgAN group with abnormal renal function were identified as Enterococcaceae, Moraxella, Moraxella, and Acinetobacter. KEGG functional analysis demonstrated that the functional pathways of the microbiota that differed between IgAN patients and healthy controls were related primarily to bile acid metabolism.<br><br>CONCLUSIONS: The status of the gut microbiota is closely associated not only with the onset of IgAN but also with the renal function of IgAN patients. The characteristic gut microbiota may serve as a promising diagnostic biomarker and therapeutic target for IgAN.},
}
@article {pmid39176710,
year = {2024},
author = {Sy, MA and Prosperi, M and Serajian, M and Boucher, C and Benos, PT and Marini, S},
title = {Prediction of A. Baumannii Amikacin Resistance in Clinical Metagenomics.},
journal = {Studies in health technology and informatics},
volume = {316},
number = {},
pages = {212-213},
doi = {10.3233/SHTI240381},
pmid = {39176710},
issn = {1879-8365},
mesh = {*Amikacin/pharmacology/therapeutic use ; *Metagenomics ; *Acinetobacter baumannii/drug effects/genetics ; Humans ; *Drug Resistance, Bacterial/genetics ; Respiratory Tract Infections/drug therapy/microbiology ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Acinetobacter Infections/drug therapy/microbiology ; },
abstract = {Respiratory tract infections are a serious threat to health, especially in the presence of antimicrobial resistance (AMR). Existing AMR detection methods are limited by slow turnaround times and low accuracy due to the presence of false positives and negatives. In this study, we simulate 1,116 clinical metagenomics samples on both Illumina and Nanopore sequencing from curated, real-world sequencing of A. baumannii respiratory infections and build AI models to predict resistance to amikacin. The best performance is achieved by XGBoost on Illumina sequencing (area under the ROC curve = 0.7993 on 5-fold cross-validation).},
}
@article {pmid39176455,
year = {2024},
author = {Li, Y and Wang, GQ and Ma, XL and Li, YB},
title = {A rare case of acute meningitis caused by Moraxella osloensis.},
journal = {CNS neuroscience &amp; therapeutics},
volume = {30},
number = {8},
pages = {e70011},
pmid = {39176455},
issn = {1755-5949},
support = {2019QL013//Academic promotion programme of Shandong First Medical University/ ; ZR2023MH127//Nature Science Foundation of Shandong/ ; },
mesh = {Humans ; *Moraxella/isolation &amp; purification/genetics ; *Moraxellaceae Infections/diagnosis/drug therapy/microbiology/complications ; *Meningitis, Bacterial/diagnosis/microbiology/drug therapy ; Male ; Female ; },
abstract = {Meningitis caused by Moraxella osloensis is rare and easily misdiagnosed clinically. Here, we report the first case of meningitis caused by M. osloensis in China by taking advantage of the metagenomic next-generation sequencing technology in cerebrospinal fluid for pathogen screening. In addition, we extend the neurological signs, clinical symptoms, diagnostic methods, and treatment of this rare disease.},
}
@article {pmid39176082,
year = {2024},
author = {Jiang, C and He, Y and Chen, X and Xia, F and Shi, F and Xu, X and Sun, T and You, K},
title = {X-linked severe combined immunodeficiency complicated by disseminated bacillus Calmette-Guérin disease caused by a novel pathogenic mutation in exon 3 of the IL2RG gene: a case report and literature review.},
journal = {Frontiers in immunology},
volume = {15},
number = {},
pages = {1453046},
pmid = {39176082},
issn = {1664-3224},
mesh = {Humans ; Infant ; Male ; BCG Vaccine/administration &amp; dosage/adverse effects/immunology ; Exons ; *Interleukin Receptor Common gamma Subunit/genetics ; Mutation ; Mycobacterium bovis/immunology/pathogenicity ; *Tuberculosis/immunology/prevention &amp; control ; *X-Linked Combined Immunodeficiency Diseases/complications/diagnosis/genetics/immunology ; },
abstract = {X-linked severe combined immunodeficiency (X-SCID), caused by mutations in the gamma-chain gene of the interleukin-2 receptor (IL2RG), is a prevalent form of SCID characterized by recurrent and fatal opportunistic infections that occur early in life. The incidence of disseminated bacillus Calmette-Guérin (BCG) disease among children with SCID is much higher than in the general population. Here, we report the case of a 4-month-old male infant who presented with subcutaneous induration, fever, an unhealed BCG vaccination site, and hepatosplenomegaly. Metagenomic next-generation sequencing in blood, and the detection of gastric juice and skin nodule pus all confirmed the infection of Mycobacterium tuberculosis. Lymphocyte subset analysis confirmed the presence of T-B+NK immunodeficiency. Whole-exome and Sanger sequencing revealed a novel microdeletion insertion mutation (c.316_318delinsGTGAT p.Leu106ValfsTer42) in the IL2RG gene, resulting in a rare shift in the amino acid sequence of the coding protein. Consequently, the child was diagnosed with X-SCID caused by a novel mutation in IL2RG, complicated by systemic disseminated BCG disease. Despite receiving systemic anti-infection treatment and four days of hospitalization, the patient died three days after discharge. To the best of our knowledge, this specific IL2RG mutation has not been previously reported. In our systemic review, we outline the efficacy of systemic anti-tuberculosis therapy, hematopoietic stem cell transplantation, and gene therapy in children with SCID and BCG diseases caused by IL2RG gene mutation.},
}
@article {pmid39175669,
year = {2024},
author = {Zhan, L and Lv, Z and Zhang, Y and Chen, J and Wang, L and Huang, R and Sun, Y and Wu, W},
title = {Use of Metagenomic Next-Generation Sequencing to Identify Pathogens Involved in Central Nervous System Infections.},
journal = {Infection and drug resistance},
volume = {17},
number = {},
pages = {3605-3615},
pmid = {39175669},
issn = {1178-6973},
abstract = {PURPOSE: Application of metagenomic next-generation sequencing (mNGS) in identifying nosocomial central nervous system (CNS) infections in critical care units remains understudied.<br><br>METHODS: We conducted a retrospective analysis of microbiological results through both mNGS and routine examination of cerebrospinal fluid (CSF) samples from patients with nosocomial CNS infections. The aim of this study was to assess the clinical diagnostic effect of nosocomial mNGS in this population.<br><br>RESULTS: The study included 26 cases of nosocomial CNS infections in total. A total of 69.2% (18/26) of the samples tested positive for mNGS, which is substantially greater than the 7.7% (2/26; p<0.05) detected through conventional techniques. Administration of antibiotics before culture is most likely the cause of the low CSF culture rate. Twenty-five pathogenic strains that were missed by standard testing. Three pathogens that were consistent with the mNGS results were positive by routine tests. Eight cases were negative by mNGS due to low pathogen CSF titres. Compared to traditional testing, mNGS demonstrated 100% sensitivity and 33.3% specificity in diagnosing CNS infections. The thirty-day mortality rate was 26.9% (7/26).<br><br>CONCLUSION: Routine microbiologic testing frequently falls short of detecting all neuroinvasive pathogens. Our research suggests that mNGS offers an alternative means of detecting nosocomial CNS infections. By applying mNGS to CSF samples from patients with meningitis or encephalitis, we were able to improve the ability to diagnose nosocomial neurologic infections.},
}
@article {pmid39175323,
year = {2024},
author = {Zhu, J and Sun, J and Ma, B and Zhang, C and Cao, X and Zheng, S and Chen, Z and Zhang, C and Shen, J and Xia, T},
title = {[Study on effectiveness of antibiotics guided by metagenomic next-generation sequencing to control infection after total knee arthroplasty].},
journal = {Zhongguo xiu fu chong jian wai ke za zhi = Zhongguo xiufu chongjian waike zazhi = Chinese journal of reparative and reconstructive surgery},
volume = {38},
number = {8},
pages = {995-1000},
pmid = {39175323},
issn = {1002-1892},
mesh = {Humans ; *Arthroplasty, Replacement, Knee/adverse effects ; Male ; Aged ; Female ; Middle Aged ; *Prosthesis-Related Infections/microbiology/diagnosis ; *Anti-Bacterial Agents/therapeutic use ; Aged, 80 and over ; Adult ; *High-Throughput Nucleotide Sequencing ; *Metagenomics/methods ; C-Reactive Protein/analysis ; Knee Prosthesis/adverse effects ; },
abstract = {OBJECTIVE: To explore the clinical value of metagenomic next-generation sequencing (mNGS) in diagnosis and treatment of periprosthetic joint infection (PJI) after total knee arthroplasty (TKA).<br><br>METHODS: Between April 2020 and March 2023, 10 patients with PJI after TKA were admitted. There were 3 males and 7 females with an average age of 69.9 years (range, 44-83 years). Infection occurred after 8-35 months of TKA (mean, 19.5 months). The duration of infection ranged from 16 to 128 days (mean, 37 days). The preoperative erythrocyte sedimentation rate (ESR) was 15-85 mm/1 h (mean, 50.2 mm/1 h). The C reactive protein (CRP) was 4.4-410.0 mg/L (mean, 192.8 mg/L). The white blood cell counting was (3.4-23.8)&#xd7;10 [9]/L (mean, 12.3&#xd7;10 [9]/L). The absolute value of neutrophils was (1.1-22.5)&#xd7;10 [9]/L (mean, 9.2&#xd7;10 [9]/L). After admission, the joint fluid was extracted for bacterial culture method and mNGS test, and sensitive antibiotics were chosen according to the results of the test, and the infection was controlled in combination with surgery.<br><br>RESULTS: Seven cases (70%) were detected as positive by bacterial culture method, and 7 types of pathogenic bacteria were detected; the most common pathogenic bacterium was Streptococcus lactis arrestans. Ten cases (100%) were detected as positive by mNGS test, and 11 types of pathogenic bacteria were detected; the most common pathogenic bacterium was Propionibacterium acnes. The difference in the positive rate between the two methods was significant (P=0.211). Three of the 7 patients who were positive for both the bacterial culture method and the mNGS test had the same results for the type of pathogenic bacteria, with a compliance rate of 42.86% (3/7). The testing time (from sample delivery to results) was (4.95&#xb1;2.14) days for bacterial culture method and (1.60&#xb1;0.52) days for mNGS test, and the difference was significant (t=4.810, P<0.001). The corresponding sensitive antibiotic treatment was chosen according to the results of bacterial culture method and mNGS test. At 3 days after the one-stage operation, the CRP was 6.8-48.2 mg/L (mean, 23.6 mg/L); the ESR was 17-53 mm/1 h (mean, 35.5 mm/1 h); the white blood cell counting was (4.5-8.1)&#xd7;10 [9]/L (mean, 6.1&#xd7;10 [9]/L); the absolute value of neutrophils was (2.3-5.7)&#xd7;10 [9]/L (mean, 4.1&#xd7;10 [9]/L). All patients were followed up 12-39 months (mean, 23.5 months). One case had recurrence of infection at 6 months after operation, and the remaining 9 cases showed no signs of infection, with an infection control rate of 90%.<br><br>CONCLUSION: Compared with bacterial culture method, mNGS test can more rapidly and accurately detect pathogenic bacteria for PJI after TKA, which is important for guiding antibiotics combined with surgical treatment of PJI.},
}
@article {pmid39175129,
year = {2024},
author = {Hotchkiss, MZ and Forrest, JRK and Poulain, AJ},
title = {Changes in bumblebee queen gut microbiotas during and after overwintering diapause.},
journal = {Insect molecular biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/imb.12957},
pmid = {39175129},
issn = {1365-2583},
support = {//Natural Sciences and Engineering Research Council of Canada/ ; },
abstract = {Bumblebees are key pollinators with gut microbiotas that support host health. After bumblebee queens undergo winter diapause, which occurs before spring colony establishment, their gut microbiotas are disturbed, but little is known about community dynamics during diapause itself. Queen gut microbiotas also help seed worker microbiotas, so it is important that they recover post-diapause to a typical community structure, a process that may be impeded by pesticide exposure. We examined how bumblebee queen gut microbiota community structure and metabolic potential shift during and after winter diapause, and whether post-diapause recovery is affected by pesticide exposure. To do so, we placed commercial Bombus impatiens queens into diapause, euthanizing them at 0, 2 and 4 months of diapause. Additionally, we allowed some queens to recover from diapause for 1 week before euthanasia, exposing half to the common herbicide glyphosate. Using whole-community, shotgun metagenomic sequencing, we found that core bee gut phylotypes dominated queen gut microbiotas before, during and after diapause, but that two phylotypes, Schmidhempelia and Snodgrassella, ceased to be detected during late diapause and recovery. Despite fluctuations in taxonomic community structure, metabolic potential remained constant through diapause and recovery. Also, glyphosate exposure did not affect post-diapause microbiota recovery. However, metagenomic assembly quality and our ability to detect microbial taxa and metabolic pathways declined alongside microbial abundance, which was substantially reduced during diapause. Our study offers new insights into how bumblebee queen gut microbiotas change taxonomically and functionally during a key life stage and provides guidance for future microbiota studies in diapausing bumblebees.},
}
@article {pmid39175061,
year = {2024},
author = {Carrascosa-Sàez, M and Buigues, J and Viñals, A and Andreu-Moreno, I and Martínez-Recio, R and Soriano-Tordera, C and Monrós, JS and Cuevas, JM and Sanjuán, R},
title = {Genetic diversity and cross-species transmissibility of bat-associated picornaviruses from Spain.},
journal = {Virology journal},
volume = {21},
number = {1},
pages = {193},
pmid = {39175061},
issn = {1743-422X},
support = {PRE2021-099824//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2020-118602RB-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; CIAICO/2022/110//Conselleria de Educaci&#xf3;n, Universidades y Empleo, Generalitat Valenciana, Spain/ ; },
mesh = {*Chiroptera/virology ; Animals ; Spain ; *Picornaviridae/genetics/classification/isolation &amp; purification ; *Genetic Variation ; *Genome, Viral ; *Phylogeny ; *Feces/virology ; *Picornaviridae Infections/transmission/virology/veterinary ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Humans ; Zoonoses/virology/transmission ; },
abstract = {BACKGROUND: Emerging zoonotic diseases arise from cross-species transmission events between wild or domesticated animals and humans, with bats being one of the major reservoirs of zoonotic viruses. Viral metagenomics has led to the discovery of many viruses, but efforts have mainly been focused on some areas of the world and on certain viral families.<br><br>METHODS: We set out to describe full-length genomes of new picorna-like viruses by collecting feces from hundreds of bats captured in different regions of Spain. Viral sequences were obtained by high-throughput Illumina sequencing and analyzed phylogenetically to classify them in the context of known viruses. Linear discriminant analysis (LDA) was performed to infer likely hosts based on genome composition.<br><br>RESULTS: We found five complete or nearly complete genomes belonging to the family Picornaviridae, including a new species of the subfamily Ensavirinae. LDA suggested that these were true vertebrate viruses, rather than viruses from the bat diet. Some of these viruses were related to picornaviruses previously found in other bat species from distant geographical regions. We also found a calhevirus genome that most likely belongs to a proposed new family within the order Picornavirales, and for which genome composition analysis suggested a plant host.<br><br>CONCLUSIONS: Our findings describe new picorna-like viral species and variants circulating in the Iberian Peninsula, illustrate the wide geographical distribution and interspecies transmissibility of picornaviruses, and suggest new hosts for calheviruses.},
}
@article {pmid39175056,
year = {2024},
author = {Sbardellati, DL and Vannette, RL},
title = {Targeted viromes and total metagenomes capture distinct components of bee gut phage communities.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {155},
pmid = {39175056},
issn = {2049-2618},
support = {2023-67011-40501//U.S. Department of Agriculture/ ; 1929516//National Science Foundation/ ; },
mesh = {Bees/virology/microbiology ; Animals ; *Bacteriophages/genetics/isolation &amp; purification/classification ; *Virome ; *Metagenome ; Gastrointestinal Microbiome/genetics ; Metagenomics/methods ; Gastrointestinal Tract/microbiology/virology ; },
abstract = {BACKGROUND: Despite being among the most abundant biological entities on earth, bacteriophage (phage) remain an understudied component of host-associated systems. One limitation to studying host-associated phage is the lack of consensus on methods for sampling phage communities. Here, we compare paired total metagenomes and viral size fraction metagenomes (viromes) as methods for investigating the dsDNA viral communities associated with the GI tract of two bee species: the European honey bee Apis mellifera and the eastern bumble bee Bombus impatiens.<br><br>RESULTS: We find that viromes successfully enriched for phage, thereby increasing phage recovery, but only in honey bees. In contrast, for bumble bees, total metagenomes recovered greater phage diversity. Across both bee species, viromes better sampled low occupancy phage, while total metagenomes were biased towards sampling temperate phage. Additionally, many of the phage captured by total metagenomes were absent altogether from viromes. Comparing between bees, we show that phage communities in commercially reared bumble bees are significantly reduced in diversity compared to honey bees, likely reflecting differences in bacterial titer and diversity. In a broader context, these results highlight the complementary nature of total metagenomes and targeted viromes, especially when applied to host-associated environments.<br><br>CONCLUSIONS: Overall, we suggest that studies interested in assessing total communities of host-associated phage should consider using both approaches. However, given the constraints of virome sampling, total metagenomes may serve to sample phage communities with the understanding that they will preferentially sample dominant and temperate phage. Video Abstract.},
}
@article {pmid39174918,
year = {2024},
author = {Wang, D and Xue, D and Chen, X and Wu, X and Gao, W and Liang, X and Yuan, W and Wang, H and Wang, Q},
title = {Mycobacterium marseillense bloodstream infection combined with skin fungal infection: a case report and literature review.},
journal = {BMC infectious diseases},
volume = {24},
number = {1},
pages = {853},
pmid = {39174918},
issn = {1471-2334},
mesh = {Humans ; Male ; Middle Aged ; *Mycobacterium Infections, Nontuberculous/microbiology/drug therapy ; Dermatomycoses/microbiology/drug therapy ; Kidney Transplantation/adverse effects ; Immunocompromised Host ; Anti-Bacterial Agents/therapeutic use ; Nontuberculous Mycobacteria/isolation &amp; purification/drug effects ; Bacteremia/microbiology/drug therapy ; Mycobacterium/isolation &amp; purification/drug effects ; Skin/microbiology/pathology ; },
abstract = {BACKGROUND: Non-tuberculous mycobacteria (NTM) are present widely in the natural environment and can invade the human body through the respiratory tract, gastrointestinal tract, and skin. Immunocompromised patients are particularly prone to infection, which primarily affects multiple organs, including the lungs, lymph nodes, and skin. However, cases of NTM bloodstream infections are rare. Here, we report a rare case of Mycobacterium marseillense bloodstream infection with concurrent skin fungal infection in a patient after kidney transplantation. Related literature was reviewed to enhance the understanding of this rare condition.<br><br>CASE PRESENTATION: A 58-year-old male with a history of long-term steroid and immunosuppressant use after kidney transplantation presented with limb swelling that worsened over the past two months. Physical examination revealed redness and swelling of the skin in all four limbs, with a non-healing wound on the lower left limb. Skin tissue analysis by metagenomic next-generation sequencing (mNGS) and fungal culture indicated infection with Trichophyton rubrum. Blood culture results suggested infection with Mycobacterium marseillense. After receiving anti-NTM treatment, the patient's symptoms significantly improved, and he is currently undergoing treatment.<br><br>CONCLUSION: Mycobacterium marseillense is a NTM. Gram staining suffered from misdetection, and the acid-fast staining result was positive. This bacterium was identified by mass spectrometry and mNGS analyses. Antimicrobial susceptibility tests for NTM were performed using the broth microdilution method. The results of the susceptibility test showed that Mycobacterium marseillense was sensitive to clarithromycin, an intermediary between moxifloxacin and linezolid. Bacterial clearance requires a combination of drugs and an adequate course of treatment. NTM bloodstream infections are relatively rare, and early identification and proactive intervention are key to their successful management.},
}
@article {pmid39174663,
year = {2024},
author = {Jafari, M and Moghimi, H and Tirandaz, H and Ebrahim-Habibi, MB},
title = {Corrosion behavior of predominant Halodesulfovibrio in a marine SRB consortium and its mitigation using ZnO nanoparticles.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {19545},
pmid = {39174663},
issn = {2045-2322},
mesh = {Corrosion ; *Zinc Oxide/chemistry/pharmacology ; *Biofilms/drug effects ; *Bioreactors/microbiology ; Steel/chemistry ; Nanoparticles/chemistry ; Microbial Consortia/drug effects ; },
abstract = {Formation of Sulfate Reducing Bacteria (SRB) biofilm accelerates microbiologically influenced corrosion (MIC). The aim of this study was to investigate both the corrosivity of a marine SRB consortium on carbon steel coupons and its mitigation in the presence of ZnO. Metagenomics analysis revealed that Halodesulfovibrio (78.9%) was predominant and could be related to MIC. The analysis also showed a remarkable shift from a highly corrosive SRB consortium in the control bioreactors to a far less corrosive consortium when ZnO was added to the bioreactors. Further results indicated that the corrosion rate of the SRB consortium was 8.17 mpy on the carbon steel coupons. In the ZnO-treated bioreactors, the count of SRB and MIC in the carbon steel coupons simultaneously reduced. Moreover, Confocal Laser Scanning Microscopy and profilometry analysis determined that ZnO could significantly decrease the amount of biofilm and the corrosion rate. Electrochemical experiments revealed higher corrosion current density (icorr) and lower charge transfer resistance (Rct) in the control bioreactors relative to the ZnO-treated bioreactors. We introduce Halodesulfovibrio as a potentially important corrosive genus in a marine SRB consortium. Additionally, ZnO could be considered a proper candidate to control the corrosion induced by Halodesulfovibrio.},
}
@article {pmid39173973,
year = {2024},
author = {Oliver, A and Alkan, Z and Stephensen, CB and Newman, JW and Kable, ME and Lemay, DG},
title = {Diet, Microbiome, and Inflammation Predictors of Fecal and Plasma Short-Chain Fatty Acids in Humans.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tjnut.2024.08.012},
pmid = {39173973},
issn = {1541-6100},
abstract = {BACKGROUND: Gut microbes produce short-chain fatty acids (SCFAs), which are associated with broad health benefits. However, it is not fully known how diet and/or the gut microbiome could be modulated to improve SCFA production.<br><br>OBJECTIVES: The objective of this study was to identify dietary, inflammatory, and/or microbiome predictors of SCFAs in a cohort of healthy adults.<br><br>METHODS: SCFAs were measured in fecal and plasma samples from 359 healthy adults in the United States Department of Agriculture Nutritional Phenotyping Study. Habitual and recent diet was assessed using a food frequency questionnaire and automated self-administered 24-h dietary assessment tool dietary recalls. Markers of systemic and gut inflammation were measured in fecal and plasma samples. The gut microbiome was assessed using shotgun metagenomics. Using statistics and machine learning, we determined how the abundance and composition of SCFAs varied with measures of diet, inflammation, and the gut microbiome.<br><br>RESULTS: We show that fecal pH may be a good proxy for fecal SCFA abundance. A higher healthy eating index for a habitual diet was associated with a compositional increase in fecal butyrate relative to acetate and propionate. SCFAs were associated with markers of subclinical gastrointestinal (GI) inflammation. Fecal SCFA abundance was inversely related to plasma lipopolysaccharide-binding protein. When we analyzed hierarchically organized diet and microbiome data with taxonomy-aware algorithms, we observed that diet and microbiome features were far more predictive of fecal SCFA abundances compared to plasma SCFA abundances. The top diet and microbiome predictors of fecal butyrate included potatoes and the thiamine biosynthesis pathway, respectively.<br><br>CONCLUSIONS: These results suggest that resistant starch in the form of potatoes and microbially produced thiamine provide a substrate and essential cofactor, respectively, for butyrate synthesis. Thiamine may be a rate-limiting nutrient for butyrate production in adults. Overall, these findings illustrate the complex biology underpinning SCFA production in the gut. This trial was registered at clinicaltrials.gov as NCT02367287.},
}
@article {pmid39173422,
year = {2024},
author = {Silva, JM and Almeida, JR},
title = {Enhancing metagenomic classification with compression-based features.},
journal = {Artificial intelligence in medicine},
volume = {156},
number = {},
pages = {102948},
doi = {10.1016/j.artmed.2024.102948},
pmid = {39173422},
issn = {1873-2860},
mesh = {*Metagenomics/methods ; *Data Compression/methods ; *Algorithms ; High-Throughput Nucleotide Sequencing/methods ; Humans ; },
abstract = {Metagenomics is a rapidly expanding field that uses next-generation sequencing technology to analyze the genetic makeup of environmental samples. However, accurately identifying the organisms in a metagenomic sample can be complex, and traditional reference-based methods may need to be more effective in some instances. In this study, we present a novel approach for metagenomic identification, using data compressors as a feature for taxonomic classification. By evaluating a comprehensive set of compressors, including both general-purpose and genomic-specific, we demonstrate the effectiveness of this method in accurately identifying organisms in metagenomic samples. The results indicate that using features from multiple compressors can help identify taxonomy. An overall accuracy of 95% was achieved using this method using an imbalanced dataset with classes with limited samples. The study also showed that the correlation between compression and classification is insignificant, highlighting the need for a multi-faceted approach to metagenomic identification. This approach offers a significant advancement in the field of metagenomics, providing a reference-less method for taxonomic identification that is both effective and efficient while revealing insights into the statistical and algorithmic nature of genomic data. The code to validate this study is publicly available at https://github.com/ieeta-pt/xgTaxonomy.},
}
@article {pmid39173390,
year = {2024},
author = {Pan, P and Gu, Y and Li, T and Zhou, NY and Xu, Y},
title = {Deciphering the triclosan degradation mechanism in Sphingomonas sp. strain YL-JM2C: Implications for wastewater treatment and marine resources.},
journal = {Journal of hazardous materials},
volume = {478},
number = {},
pages = {135511},
doi = {10.1016/j.jhazmat.2024.135511},
pmid = {39173390},
issn = {1873-3336},
mesh = {*Triclosan/metabolism ; *Sphingomonas/metabolism/genetics ; *Biodegradation, Environmental ; *Wastewater ; Water Pollutants, Chemical/metabolism ; Molecular Docking Simulation ; Dioxygenases/metabolism/genetics ; Bacterial Proteins/metabolism/genetics ; Anti-Infective Agents, Local/metabolism ; Waste Disposal, Fluid/methods ; },
abstract = {Triclosan (TCS), an antimicrobial agent extensively incorporated into pharmaceuticals and personal care products, poses significant environmental risks because of its persistence and ecotoxicity. So far, a few microorganisms were suggested to degrade TCS, but the microbial degradation mechanism remains elusive. Here, a two-component angular dioxygenase (TcsAaAb) responsible for the initial TCS degradation was characterized in Sphingomonas sp. strain YL-JM2C. Whole-cell biotransformation and crude enzyme assays demonstrated that TcsAaAb catalyzed the conversion of TCS to 4-chlorocatechol and 3,5-dichlorocatechol rather than the commonly suggested product 2,4-dichlorophenol. Then two intermediates were catabolized by tcsCDEF cluster via an ortho-cleavage pathway. Critical residues (N262, F279, and F391) for substrate binding were identified via molecular docking and mutagenesis. Further, TcsAaAb showed activity toward methyl triclosan and nitrofen, suggesting its versatile potential for bioremediation. In addition, TCS-degrading genes were also present in diverse bacterial genomes in wastewater, ocean and soil, and a relatively high gene abundance was observed in marine metagenomes, revealing the transformation fate of TCS in environments and the microbial potential in pollutant removal. These findings extend the understanding of the microbe-mediated TCS degradation and contribute to the mining of TCS-degrading strains and enzymes, as well as their application in the bioremediation of contaminated environments.},
}
@article {pmid39173381,
year = {2024},
author = {Hu, S and Xu, C and Lu, P and Wu, M and Chen, A and Zhang, M and Xie, Y and Han, G},
title = {Widespread distribution of the DyP-carrying bacteria involved in the aflatoxin B1 biotransformation in Proteobacteria and Actinobacteria.},
journal = {Journal of hazardous materials},
volume = {478},
number = {},
pages = {135493},
doi = {10.1016/j.jhazmat.2024.135493},
pmid = {39173381},
issn = {1873-3336},
mesh = {*Aflatoxin B1/metabolism ; *Actinobacteria/metabolism/genetics ; *Proteobacteria/metabolism/genetics ; *Biotransformation ; Paracoccus/metabolism/genetics ; Biodegradation, Environmental ; },
abstract = {Aflatoxin is one of the most notorious mycotoxins, of which aflatoxin B1 (AFB1) is the most harmful and prevalent. Microbes play a crucial role in the environment for the biotransformation of AFB1. In this study, a bacterial consortium, HS-1, capable of degrading and detoxifying AFB1 was obtained. Here, we combined multi-omics and cultivation-based techniques to elucidate AFB1 biotransformation by consortium HS-1. Co-occurrence network analysis revealed that the key taxa responsible for AFB1 biotransformation in consortium HS-1 mainly belonged to the phyla Proteobacteria and Actinobacteria. Moreover, metagenomic analysis showed that diverse microorganisms, mainly belonging to the phyla Proteobacteria and Actinobacteria, carry key functional enzymes involved in the initial step of AFB1 biotransformation. Metatranscriptomic analysis indicated that Paracoccus-related bacteria were the most active in consortium HS-1. A novel bacterium, Paracoccus sp. strain XF-30, isolated from consortium HS-1, contains a novel dye-decolorization peroxidase (DyP) enzyme capable of effectively degrading AFB1. Taxonomic profiling by bioinformatics revealed that DyP, which is involved in the initial biotransformation of AFB1, is widely distributed in metagenomes from various environments, primarily taxonomically affiliated with Proteobacteria and Actinobacteria. The in-depth examination of AFB1 biotransformation in consortium HS-1 will help us to explore these crucial bioresources more sensibly and efficiently.},
}
@article {pmid39173358,
year = {2024},
author = {Chen, X and Duan, F and Yu, X and Xie, Y and Wang, Z and El-Baz, A and Ni, BJ and Ni, SQ},
title = {One-stage anammox and thiocyanate-driven autotrophic denitrification for simultaneous removal of thiocyanate and nitrogen: Pathway and mechanism.},
journal = {Water research},
volume = {265},
number = {},
pages = {122268},
doi = {10.1016/j.watres.2024.122268},
pmid = {39173358},
issn = {1879-2448},
mesh = {*Denitrification ; *Thiocyanates/metabolism ; *Nitrogen/metabolism ; *Autotrophic Processes ; Bioreactors ; Wastewater/chemistry ; Waste Disposal, Fluid/methods ; Sewage ; Oxidation-Reduction ; Anaerobiosis ; },
abstract = {The coupled process of anammox and reduced-sulfur driven autotrophic denitrification can simultaneously remove nitrogen and sulfur from wastewater, while minimizing energy consumption and sludge production. However, the research on the coupled process for removing naturally toxic thiocyanate (SCN[-]) is limited. This work successfully established and operated a one-stage coupled system by co-cultivating mature anammox and SCN[-]-driven autotrophic denitrification sludge in a single reactor. In this one-stage coupled system, the average total nitrogen removal efficiency was 89.68±3.33 %, surpassing that of solo anammox (81.80±2.10 %) and SCN[-]-driven autotrophic denitrification (85.20±1.54 %). Moreover, the average removal efficiency of SCN[-] reached 99.50±3.64 %, exceeding that of solo SCN[-]-driven autotrophic denitrification (98.80±0.65 %). The results of the [15]N stable isotope tracer labeling experiment revealed the respective reaction rates of anammox and denitrification as 106.38±10.37 μmol/L/h and 69.07±8.07 μmol/L/h. By analyzing metagenomic sequencing data, Thiobacillus_denitrificans was identified as the primary contributor to SCN[-] degradation in this coupled system. Furthermore, based on the comprehensive analysis of nitrogen and sulfur metabolic pathways, as well as the genes associated with SCN[-] degradation, it can be inferred that the cyanate (CNO) pathway was responsible for SCN[-] degradation. This work provided a deeper insight into coupling anammox with SCN[-]-driven autotrophic denitrification in a one-stage coupled system, thereby contributing to the development of an effective approach for wastewater treatment involving both SCN[-] and nitrogen.},
}
@article {pmid39173234,
year = {2024},
author = {Jia, P and Liang, JL and Lu, JL and Zhong, SJ and Xiong, T and Feng, SW and Wang, Y and Wu, ZH and Yi, XZ and Gao, SM and Zheng, J and Wen, P and Li, F and Li, Y and Liao, B and Shu, WS and Li, JT},
title = {Soil keystone viruses are regulators of ecosystem multifunctionality.},
journal = {Environment international},
volume = {191},
number = {},
pages = {108964},
doi = {10.1016/j.envint.2024.108964},
pmid = {39173234},
issn = {1873-6750},
mesh = {*Soil Microbiology ; China ; *Ecosystem ; *Viruses/genetics ; Soil/chemistry ; Microbiota ; Fungi/genetics ; Forests ; Metagenomics ; Biodiversity ; },
abstract = {Ecosystem multifunctionality reflects the capacity of ecosystems to simultaneously maintain multiple functions which are essential bases for human sustainable development. Whereas viruses are a major component of the soil microbiome that drive ecosystem functions across biomes, the relationships between soil viral diversity and ecosystem multifunctionality remain under-studied. To address this critical knowledge gap, we employed a combination of amplicon and metagenomic sequencing to assess prokaryotic, fungal and viral diversity, and to link viruses to putative hosts. We described the features of viruses and their potential hosts in 154 soil samples from 29 farmlands and 25 forests distributed across China. Although 4,460 and 5,207 viral populations (vOTUs) were found in the farmlands and forests respectively, the diversity of specific vOTUs rather than overall soil viral diversity was positively correlated with ecosystem multifunctionality in both ecosystem types. Furthermore, the diversity of these keystone vOTUs, despite being 10-100 times lower than prokaryotic or fungal diversity, was a better predictor of ecosystem multifunctionality and more strongly associated with the relative abundances of prokaryotic genes related to soil nutrient cycling. Gemmatimonadota and Actinobacteria dominated the host community of soil keystone viruses in the farmlands and forests respectively, but were either absent or showed a significantly lower relative abundance in that of soil non-keystone viruses. These findings provide novel insights into the regulators of ecosystem multifunctionality and have important implications for the management of ecosystem functioning.},
}
@article {pmid39172545,
year = {2024},
author = {Chen, G and Jiang, J and Sun, Y},
title = {RNAVirHost: a machine learning-based method for predicting hosts of RNA viruses through viral genomes.},
journal = {GigaScience},
volume = {13},
number = {},
pages = {},
pmid = {39172545},
issn = {2047-217X},
support = {//Research Grants Council, University Grants Committee/ ; },
mesh = {*Machine Learning ; *Genome, Viral ; *RNA Viruses/genetics/classification ; High-Throughput Nucleotide Sequencing/methods ; Computational Biology/methods ; Software ; },
abstract = {BACKGROUND: The high-throughput sequencing technologies have revolutionized the identification of novel RNA viruses. Given that viruses are infectious agents, identifying hosts of these new viruses carries significant implications for public health and provides valuable insights into the dynamics of the microbiome. However, determining the hosts of these newly discovered viruses is not always straightforward, especially in the case of viruses detected in environmental samples. Even for host-associated samples, it is not always correct to assign the sample origin as the host of the identified viruses. The process of assigning hosts to RNA viruses remains challenging due to their high mutation rates and vast diversity.<br><br>RESULTS: In this study, we introduce RNAVirHost, a machine learning-based tool that predicts the hosts of RNA viruses solely based on viral genomes. RNAVirHost is a hierarchical classification framework that predicts hosts at different taxonomic levels. We demonstrate the superior accuracy of RNAVirHost in predicting hosts of RNA viruses through comprehensive comparisons with various state-of-the-art techniques. When applying to viruses from novel genera, RNAVirHost achieved the highest accuracy of 84.3%, outperforming the alignment-based strategy by 12.1%.<br><br>CONCLUSIONS: The application of machine learning models has proven beneficial in predicting hosts of RNA viruses. By integrating genomic traits and sequence homologies, RNAVirHost provides a cost-effective and efficient strategy for host prediction. We believe that RNAVirHost can greatly assist in RNA virus analyses and contribute to pandemic surveillance.},
}
@article {pmid39171911,
year = {2024},
author = {Quan, Q and Liu, J and Xia, X and Zhang, S and Ke, Z and Wang, M and Tan, Y},
title = {Cold seep nitrogen fixation and its potential relationship with sulfur cycling.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0053624},
doi = {10.1128/spectrum.00536-24},
pmid = {39171911},
issn = {2165-0497},
abstract = {UNLABELLED: Dinitrogen (N2) fixation is a crucial source of bioavailable nitrogen in carbon-dominated cold seep systems. Previous studies have shown that diazotrophy is not necessarily dependent on sulfate-dependent anaerobic oxidation of methane for energy, and diverse catabolism can fuel the high-energy-demanding process in sediments. However, it remains unclear whether diazotroph can obtain energy by sulfur oxidation in sulfur-rich cold seep water column. Here, field investigations and in situ experiments were conducted in Haima cold seep to examine the effects of diverse sources of dissolved organic matter (DOM) on N2 fixation, specifically containing sulfur, carbon, nitrogen, and phosphorus. We found that active N2 fixation occurred in the water column above the Haima cold seep, with the Dechloromonas genus dominating the diazotroph community as revealed by nifH gene using high-throughput sequencing. In situ experiments showed an increased rate of N2 fixation (1.15- to 12.70-fold compared to that in control group) and a greater relative abundance of the Dechloromonas genus following enrichment with sulfur-containing organic matter. Furthermore, metagenomic assembly and binning revealed that Dechloromonas sp. carried genes related to N2 fixation (nifDHK) and sulfur compound oxidation (fccAB and soxABCXYZ), implying that the genus potentially serves as a multifunctional mediator for N2 fixation and sulfur cycling. Our results provide new insights regarding potential coupling mechanism associated with sulfur-driven N2 fixation in methane- and sulfide-rich environments.<br><br>IMPORTANCE: N2 fixation is an important source of biologically available in carbon-dominated cold seep systems as little nitrogen is released by hydrocarbon seepage, thereby promoting biological productivity and the degradation of non-nitrogenous organic matter. Cold seeps are rich in diverse sources of dissolved organic matter (DOM) derived from the sinking of photosynthetic products in euphotic layer and the release of chemosynthesis products on the seafloor. However, it remains unclear whether N2 fixation is coupled to the metabolic processes of DOM, as determined by e.g., carbon, nitrogen, phosphorus, and sulfur content, for energy acquisition in sulfur-rich cold seeps. In this study, diazotroph community structure and its response to DOM compositions were revealed. Moreover, the metagenomics analysis suggested that Dechloromonas genus plays a dominant role in potential coupling N2 fixation and sulfur oxidation. Our study highlighted that sulfur oxidation in deep-sea cold seeps may serve as an energy source to drive N2 fixation.},
}
@article {pmid39171900,
year = {2024},
author = {, },
title = {Expression of Concern for Huang et al., "Long-Read Metagenomics of Marine Microbes Reveals Diversely Expressed Secondary Metabolites".},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0185124},
doi = {10.1128/spectrum.01851-24},
pmid = {39171900},
issn = {2165-0497},
}
@article {pmid39170984,
year = {2024},
author = {Rajendhran, J and Muthuirulan, P and Lakshmanan, AP and Sundararaju, S},
title = {Editorial: Clinical metagenomics-based diagnostics for infectious diseases.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1459621},
pmid = {39170984},
issn = {2235-2988},
mesh = {*Metagenomics/methods ; Humans ; *Communicable Diseases/diagnosis ; },
}
@article {pmid39170962,
year = {2024},
author = {Yue, M and Tao, S and Gaietto, K and Chen, W},
title = {Omics approaches in asthma research: Challenges and opportunities.},
journal = {Chinese medical journal pulmonary and critical care medicine},
volume = {2},
number = {1},
pages = {1-9},
pmid = {39170962},
issn = {2772-5588},
support = {K12 HD052892/HD/NICHD NIH HHS/United States ; },
abstract = {Asthma, a chronic respiratory disease with a global prevalence of approximately 300 million individuals, presents a significant societal and economic burden. This multifaceted syndrome exhibits diverse clinical phenotypes and pathogenic endotypes influenced by various factors. The advent of omics technologies has revolutionized asthma research by delving into the molecular foundation of the disease to unravel its underlying mechanisms. Omics technologies are employed to systematically screen for potential biomarkers, encompassing genes, transcripts, methylation sites, proteins, and even the microbiome components. This review provides an insightful overview of omics applications in asthma research, with a special emphasis on genetics, transcriptomics, epigenomics, and the microbiome. We explore the cutting-edge methods, discoveries, challenges, and potential future directions in the realm of asthma omics research. By integrating multi-omics and non-omics data through advanced statistical techniques, we aspire to advance precision medicine in asthma, guiding diagnosis, risk assessment, and personalized treatment strategies for this heterogeneous condition.},
}
@article {pmid39170784,
year = {2024},
author = {Li, K and Lin, H and Han, M and Yang, L},
title = {Soil metagenomics reveals the effect of nitrogen on soil microbial communities and nitrogen-cycle functional genes in the rhizosphere of Panax ginseng.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1411073},
pmid = {39170784},
issn = {1664-462X},
abstract = {Nitrogen (N) is the primary essential nutrient for ginseng growth, and a reasonable nitrogen application strategy is vital for maintaining the stability of soil microbial functional communities. However, how microbial-mediated functional genes involved in nitrogen cycling in the ginseng rhizosphere respond to nitrogen addition is largely unknown. In this study, metagenomic technology was used to study the effects of different nitrogen additions (N0: 0, N1: 20, N2: 40 N g/m[2]) on the microbial community and functional nitrogen cycling genes in the rhizosphere soil of ginseng, and soil properties related to the observed changes were evaluated. The results showed that N1 significantly increased the soil nutrient content compared to N0, and the N1 ginseng yield was the highest (29.90% and 38.05% higher than of N0 and N2, respectively). N2 significantly decreased the soil NO3 [-]N content (17.18 mg/kg lower than N0) and pH. This resulted in a decrease in the diversity of soil microorganisms, a decrease in beneficial bacteria, an increase in the number of pathogenic microorganisms, and an significant increase in the total abundance of denitrification, assimilatory nitrogen reduction, and dissimilatory nitrogen reduction genes, as well as the abundance of nxrA and napA genes (17.70% and 65.25% higher than N0, respectively), which are functional genes involved in nitrification that promote the soil nitrogen cycling process, and reduce the yield of ginseng. The results of the correlation analysis showed that pH was correlated with changes in the soil microbial community, and the contents of soil total nitrogen (TN), ammonium nitrogen (NH4 [+]-N), and alkaline-hydrolyzed nitrogen (AHN) were the main driving factors affecting the changes in nitrogen cycling functional genes in the rhizosphere soil of ginseng. In summary, nitrogen addition affects ginseng yield through changes in soil chemistry, nitrogen cycling processes, and functional microorganisms.},
}
@article {pmid39170756,
year = {2024},
author = {Bumrungthai, S and Duangjit, S and Passorn, S and Pongpakdeesakul, S and Butsri, S and Janyakhantikul, S},
title = {Comprehensive breast cancer risk analysis with whole exome sequencing and the prevalence of BRCA1 and ABCG2 mutations and oncogenic HPV.},
journal = {Biomedical reports},
volume = {21},
number = {4},
pages = {144},
pmid = {39170756},
issn = {2049-9442},
abstract = {Breast cancer is the most prevalent cancer and also the leading cause of cancer death in women worldwide. A comprehensive understanding of breast cancer risk factors and their incidences is useful information for breast cancer prevention and control planning. The present study aimed to provide information on single nucleotide polymorphisms (SNPs) and copy number variations (CNVs) in breast cancer, the allele frequency of two SNPs in breast cancer-related genes BRCA1 DNA repair associated (BRCA1; rs799917) and ATP binding cassette subfamily G member 2 (ABCG2; rs2231142), and the prevalence of human papillomavirus (HPV) infections in a normal population living in Phayao Province, Northern Thailand. One breast cancer and 10 healthy samples were investigated by whole exome sequencing (WES) and compared for genetic variation. The WES data contained SNPs in genes previously implicated in breast cancer and provided data on CNVs. The allele frequencies for SNPs rs799917 and rs2231142 were also examined. The SNP genotype frequencies were 35.88% CC, 46.54% CT, and 17.58% TT for rs799917 and 33.20% CC, 46.88% CA, and 19.92% AA for rs2231142. A total of 825 human whole blood samples were examined for HPV infection by PCR, and the pooled DNA was tested for HPV infection using metagenomic sequencing. No HPV infections were detected among all 825 samples or the pooled blood samples. The incidence of breast cancer among the tested samples was estimated based on acceptable breast cancer risk factors and demographic data and was 1.47%. The present study provided data on SNPs and CNVs in breast cancer-related genes. The associations between SNPs rs2231142 and rs799917 and breast cancer should be further investigated in a case-control study since heterozygous and homozygous variants are more common. Based on the detection of HPV infection in the blood samples, HPV may not be associated with breast cancer, at least in the Northern Thai population.},
}
@article {pmid39170755,
year = {2024},
author = {Li, S and Zhang, Y and Han, D},
title = {Severe community‑acquired pneumonia caused by Legionella gormanii in combination with influenza A subtype (H1N1) virus in an immunocompetent patient detected by metagenomic next‑generation sequencing: A case report.},
journal = {Biomedical reports},
volume = {21},
number = {4},
pages = {145},
pmid = {39170755},
issn = {2049-9442},
abstract = {Legionella pneumonia is an atypical form of pneumonia caused by Legionella gormanii that can also lead to multiple organ diseases, including acute respiratory distress syndrome and multiple organ dysfunction syndrome. Legionella gormanii requires a long incubation period for culture in clinical practice using BCYE medium. The specificity of serum for serological detection is low, resulting in a relatively high rate of missed Legionella diagnoses. Contracting the H1N1 virus can lead to the misdiagnosis of Legionella gormanii. Metagenomic next-generation sequencing (mNGS) is a novel tool that can rapidly and accurately identify potential Legionella gormanii strains. A severe case of community-acquired pneumonia in a 79-year-old patient was reported. The patient was diagnosed with Legionella gormanii and influenza A subtype (H1N1) virus using mNGS at The First Affiliated Hospital, Zhejiang University School of Medicine. After anti-Legionella and antiviral therapy, the number of reads identifying Legionella gormanii in bronchoalveolar lavage fluid using mNGS decreased from 665 to 112 as the patient's condition gradually improved. A search of PubMed revealed few reports of Legionella gormanii in association with the influenza A subtype (H1N1) virus. Patients with severe pneumonia caused by Legionella and influenza A subtype H1N1 virus infections should be screened early for infections using methods such as mNGS. This approach enables early and precise treatment, simplifying the administration of antibiotics and enhancing patient outcomes.},
}
@article {pmid39170692,
year = {2024},
author = {Iwan, E and Grenda, A and Bomba, A and Bielińska, K and Wasyl, D and Kieszko, R and Rolska-Kopińska, A and Chmielewska, I and Krawczyk, P and Rybczyńska-Tkaczyk, K and Olejnik, M and Milanowski, J},
title = {Gut resistome of NSCLC patients treated with immunotherapy.},
journal = {Frontiers in genetics},
volume = {15},
number = {},
pages = {1378900},
pmid = {39170692},
issn = {1664-8021},
abstract = {BACKGROUND: The newest method of treatment for patients with NSCLC (non-small cell lung cancer) is immunotherapy directed at the immune checkpoints PD-1 (Programmed Cell Death 1) and PD-L1 (Programmed Cell Death Ligand 1). PD-L1 is the only validated predictor factor for immunotherapy efficacy, but it is imperfect. Some patients do not benefit from immunotherapy and may develop primary or secondary resistance. This study aimed to assess the intestinal resistome composition of non-small cell lung cancer (NSCLC) patients treated with immune checkpoint inhibitors in the context of clinical features and potentially new prediction factors for assessing immunotherapy efficacy.<br><br>METHODS: The study included 30 advanced NSCLC patients, 19 (57%) men and 11 (33%) women treated with first- or second-line immunotherapy (nivolumab, pembrolizumab or atezolizumab). We evaluated the patient's gut resistome composition using the high sensitivity of targeted metagenomics.<br><br>RESULTS: Studies have shown that resistome richness is associated with clinical and demographic factors of NSCLC patients treated with immunotherapy. Smoking seems to be associated with an increased abundance of macrolides, lincosamides, streptogramins and vancomycin core resistome. The resistome of patients with progression disease appears to be more abundant and diverse, with significantly higher levels of genomic markers of resistance to lincosamides (lnuC). The resistance genes lnuC, msrD, ermG, aph(6), fosA were correlated with progression-free survival or/and overall survival, thus may be considered as factors potentially impacting the disease.<br><br>CONCLUSION: The results indicate that the intestinal resistome of NSCLC patients with immune checkpoint inhibitors treatment differs depending on the response to immunotherapy, with several distinguished markers. Since it might impact treatment efficacy, it must be examined more deeply.},
}
@article {pmid39170628,
year = {2024},
author = {Bi, B and Fu, X and Jian, X and Zhang, Y and Jiang, Y and Zhou, W and Zhao, H},
title = {Assessment of the potential risks in SD rats gavaged with genetically modified yeast containing the cp4-epsps gene.},
journal = {Frontiers in veterinary science},
volume = {11},
number = {},
pages = {1411520},
pmid = {39170628},
issn = {2297-1769},
abstract = {INTRODUCTION: Despite the absence of definitive evidence indicating that the cp4-epsps gene and its resultant recombinant proteins have significant harmful effects on either human or animal health, the safety assessment of genetically modified (GM) crops expressing the CP4-EPSPS proteins has been controversial. This study endeavor was aimed at evaluating the potential risks posed by the CP4-EPSPS protein in transgenic crops, thereby contributing to the advancement of risk assessment methodologies in the context of genetically engineered crops.<br><br>METHODS: To ascertain the appropriate daily dosages for oral gavage administration, the expression levels of the CP4-EPSPS protein in a recombinant yeast were quantified. Subsequently, physiological and biochemical analysis, metabolomics, and metagenomic analysis were conducted based on a 90-day Sprague-Dawley (SD) rats feeding experiment, respectively, thereby enhancing the depth and precision of our risk assessment framework.<br><br>RESULTS: The results from the physiological and biochemical analysis, organ pathological, blood metabolism, gut microbiota, and correlation analysis of metabolites and gut microbiota revealed several biomarkers for further risk assessment. These biomarkers include clinical biochemical indexes such as total bilirubin (TBIL), direct bilirubin (DBIL), creatine kinase (CK), and lactate dehydrogenase (LDH); metabolites like Methionine, 2-Oxovaleric acid, and LysoPC (16:0); and gut microbiota including Blautia wexlerae, Holdemanella biformis, Dorea sp. CAG 317, Coriobacteriaceae and Erysipelotrichaceae.<br><br>CONCLUSION: In conclusion, the risk can be significantly reduced by directly consuming inactivated recombinant CP4-EPSPS. Therefore, in everyday life, the risk associated with consuming GM foods containing recombinant CP4-EPSPS is substantially reduced after heat treatment.},
}
@article {pmid39170256,
year = {2024},
author = {Yuan, M and Dong, G and Han, N and Yan, L and Tang, H},
title = {Disseminated Mycobacterium tilburgii infection in a person with AIDS: A case report.},
journal = {Heliyon},
volume = {10},
number = {15},
pages = {e35616},
pmid = {39170256},
issn = {2405-8440},
abstract = {BACKGROUND: Mycobacterium tilburgii is a nonculturable, nontuberculous mycobacterium that occasionally causes serious infections in individuals with immune deficiencies. Owing to its nonculturable nature, its antimicrobial susceptibility has not been assessed, and the optimal treatment regimen is unclear. Herein, we report a case of disseminated M. tilburgii infection in a person with AIDS, identified using metagenomics next-generation sequencing (mNGS) and polymerase chain reaction (PCR).<br><br>CASE PRESENTATION: A 33-year-old man presented with a 3-month history of abdominal pain, lymphadenopathy, intermittent night hot flashes, night sweats, and weight loss. No pathogen was detected during initial routine investigations. M. tilburgii was subsequently identified in a left cervical lymph node sample using mNGS. Furthermore, M. tilburgii infection was detected in a bone marrow sample based on PCR of 16S rRNA and hsp65 gene sequencing. The person was treated with a combination of moxifloxacin, clarithromycin, ethambutol, rifabutin, and amikacin. The laboratory results improved, and the patient's symptoms resolved.<br><br>CONCLUSION: M. tilburgii may be missed in diagnostic tests because it cannot be grown using routine culture techniques. Early diagnosis and timely and effective treatment are critical in patients with M. tilburgii infection; therefore, molecular techniques are recommended for patients with suspected M. tilburgii infection.},
}
@article {pmid39170217,
year = {2024},
author = {Lu, L and Zhao, Z and Liu, C and Zhang, B and Fu, M and Wang, D and Shen, J and Cai, H and Shang, W},
title = {Multiple lymph nodes enlargement and fever as main manifestations of nocardiosis in immunocompetent individuals: Two case reports.},
journal = {Heliyon},
volume = {10},
number = {15},
pages = {e35681},
pmid = {39170217},
issn = {2405-8440},
abstract = {Nocardia farcinica is an aerobic gram-positive bacterium that is pathogenic to humans. It usually causes local and adjacent tissues' diseases at the entry of infection (most commonly occur in the lungs, skin, or central nervous system), which can also spread to other organs through the bloodstream such as joints, kidneys, and liver. However, these infections are often seen as opportunistic that occur in immunocompromised patients. Here, we report for the first time two immunocompetent patients lacking evidence of local infections, with multiple lymph node enlargements and fever as main clinical manifestations, finally diagnosed as nocardiosis by Metagenomic Next-Generation Sequencing testing (mNGS) from formalin-fixed and paraffin-embedded (FFPE) lymph node tissue, after all the other standard tests were negative. Both patients recovered after receiving anti-nocardia therapies. These two cases indicates that in healthy population, there may be more potential nocardia infections than we expected. Multiple lymph node enlargements and fever suggest a possibility of nocardiosis, especially in patients with fever of unknown origin (FUO). mNGS detection from FFPE lymph node tissue is an accurate, reliable and traceable method for diagnosis of nocardiosis.},
}
@article {pmid39170112,
year = {2024},
author = {Zhang, H and Lu, M and Guo, C and Wang, L and Ye, K and Zhao, Q and Yang, J and Yang, L and Li, T},
title = {Clinical impact of metagenomic next-generation sequencing of bronchoalveolar lavage fluids for the diagnosis of pulmonary infections in respiratory intensive care unit.},
journal = {Heliyon},
volume = {10},
number = {15},
pages = {e35287},
pmid = {39170112},
issn = {2405-8440},
abstract = {BACKGROUND: The real-world clinical impact of mNGS on BALF in the respiratory intensive care unit (RICU) is not yet fully understood.<br><br>METHODS: We investigated the clinical impact of mNGS on BALF samples obtained from 92 patients admitted to the RICU over a 2-year period. We utilized both mNGS and culture methods to evaluate the effectiveness of mNGS in diagnosing pulmonary infections. The clinical impact of mNGS were evaluated by the clinician committees.<br><br>RESULTS: Among the 92 diagnosed patients, 78 cases (84.7&#xa0;%) were determined to have infectious diseases caused by pathogenic microorganisms, and the bacterial infections constituted the most prevalent diagnostic category. For mixed infection, the most common type was the Pneumocystis jironecii and cytomegalovirus co-infection. The mNGS results had a positive impact on the clinical management of 43 cases (46.7&#xa0;%). Moreover, 19 cases (44.2&#xa0;%) of positive clinical impacts were solely based on new diagnoses made possible by mNGS results. These new diagnoses were particularly helpful for identifying rare pathogens, which could not be detected by conventional diagnostic methods.<br><br>CONCLUSIONS: The BALF mNGS has a positive real-world impact in RICU. Clinician committee play a critical role in ensuring the appropriate use of mNGS.},
}
@article {pmid39169078,
year = {2024},
author = {Lin, J and Yang, Z and Hong, Y and Cai, W and Pan, H and Lin, J and Ye, L},
title = {A novel infrared spectroscopy marker for assessing the postoperative infection risk in patients with upper urinary tract calculus.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {19398},
pmid = {39169078},
issn = {2045-2322},
support = {Grant number 2021J01398//Natural Science Foundation of Fujian Province/ ; },
mesh = {Humans ; Male ; Female ; Middle Aged ; *Spectrophotometry, Infrared ; *Postoperative Complications/etiology/diagnosis ; *Urinary Calculi/surgery ; Adult ; Urinary Tract Infections/diagnosis ; Aged ; Biomarkers/urine ; Risk Factors ; Risk Assessment/methods ; },
abstract = {The aim of this study is to evaluate the ability of infrared wavenumber of calculus to predict postoperative infection in patients with upper urinary tract calculus (UUTC), and to establish a predictive model based on this. From March 2018 to March 2023, 480 UUTC patients from Fujian Provincial Hospital were included in this study. The infrared-wavenumbers related infection score (IR-infection score) was constructed by univariate analysis, multicollinearity screening, and Lasso analysis to predict postoperative infection. Continually, the Delong test was used to compare the predictive power between the IR-infection score and traditional indicators. Afterward, we performed urine metagene sequencing and stone culture to prove the correlation between calculus toxicity and IR-infection score. Finally, logistic regression was used to build a nomogram. IR-infection score composed of four independent wavenumbers could precisely predict postoperative infection (AUCvalidation cohort = 0.707) and sepsis (AUCvalidation cohort = 0.824). IR-infection score had better predictive ability than commonly used clinical indicators. Moreover, metagenomics sequencing and calculus culture confirmed the correlation between IR-infection score and calculus toxicity (all P < 0.05). The nomogram based on the IR-infection score had high predictive power (all AUCs > 0.803). Our study first developed a novel infrared spectroscopy marker and nomogram, which can help urologists better predict postoperative infection in UUTC patients.},
}
@article {pmid39168909,
year = {2024},
author = {Wang, X and Li, Y and Kang, L and Zhang, Z and Zhang, D and Li, P and Zhang, Q and Ma, X and Wang, J and Hou, Y and Li, Q and Fu, J and Hong, M},
title = {Diversity, functions, and antibiotic resistance genes of bacteria and fungi are examined in the bamboo plant phyllosphere that serve as food for the giant pandas.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {39168909},
issn = {1618-1905},
support = {2019QZKK05010502//by the Second Qinghai-Tibet Plateau Comprehensive Scientific Survey/ ; KCXTD2022-7//the Innovation Team Funds of China West Normal University/ ; },
abstract = {The phyllosphere of bamboo is rich in microorganisms that can disrupt the intestinal microbiota of the giant pandas that consume them, potentially leading to their death. In the present study, the abundance, diversity, biological functions (e.g., KEGG and CAZyme), and antibiotic resistance genes (ARGs) of bacteria and fungi in two bamboo species phyllosphere (Chimonobambusa szechuanensis, CS; Bashania fangiana, BF) in Daxiangling Nature Reserve (an important part of the Giant Panda National Park) were investigated respectively by amplicon sequencing of the whole 16S rRNA and ITS1-ITS2 genes on PacBio Sequel and whole-metagenome shotgun sequencing on Illumina NovaSeq 6000 platform. The results suggested that there were respectively 18 bacterial and 34 fungi biomarkers between the phyllosphere of the two species of bamboo. Beta diversity of bacteria and fungi communities exited between the two bamboos according to the (un)weighted UniFrac distance matrix. Moreover, the functional analysis showed that the largest relative abundance was found in the genes related to metabolism and global and overview maps. Glycoside hydrolases (GHs) and glycosyl transferases (GTs) have a higher abundance in two bamboo phyllospheres. Co-occurrence network modeling suggested that bacteria and fungi communities in CS phyllosphere employed a much more complex metabolic network than that in BF, and the abundance of multidrug, tetracycline, and glycopeptide resistance genes was higher and closely correlated with other ARGs. This study references the basis for protecting bamboo resources foraged by wild giant pandas and predicts the risk of antibiotic resistance in bamboo phyllosphere bacterial and fungal microbiota in the Giant Panda National Park, China.},
}
@article {pmid39168671,
year = {2024},
author = {Yang, T and Wang, XY and Sui, X and Hui, XL and Wang, ZX and Jiang, B and Zhang, ZP and Li, XL},
title = {[Analysis of Antibiotic Resistance of Bioaerosols from Wastewater Treatment Process].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {45},
number = {8},
pages = {4512-4519},
doi = {10.13227/j.hjkx.202309002},
pmid = {39168671},
issn = {0250-3301},
mesh = {*Wastewater/microbiology ; *Aerosols/analysis ; *Air Microbiology ; *Waste Disposal, Fluid/methods ; Pseudomonas aeruginosa/genetics/drug effects/isolation &amp; purification ; Genes, Bacterial ; Escherichia coli/isolation &amp; purification/genetics/drug effects ; Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents ; Drug Resistance, Bacterial/genetics ; Bacteria/classification/genetics/isolation &amp; purification/drug effects ; Drug Resistance, Multiple, Bacterial/genetics ; },
abstract = {To explore the prevalence and source of antibiotic resistant genes （ARGs） and pathogenic antibiotic resistant bacteria （PARB） associated with bioaerosols in wastewater treatment plants （WWTPs）, metagenomic sequencing and assembly were applied to elucidate the antibiotic resistome of bioaerosols and wastewater in WWTPs. The results showed that more subtypes of ARGs and a higher abundance of PARB were found in bioaerosols from WWTPs and downwind than those from upwind. Multidrug and macB were respectively the most dominant type and subtype of ARGs in bioaerosols from WWTPs. In total, 37 types of PARB carried at least two or more ARG types and were characterized by multiple drug resistance. At the fine grid, aerated tank, and sludge dewatering room, wastewater was the main source of bioaerosol ARGs and PARB. A total of 32 PARB were easily aerosolized in at least one wastewater treatment unit, such as Pseudomonas aeruginosa and Escherichia coli. This study will provide theoretical support for the risk assessment and health protection of antibiotic resistant pollution associated with bioaerosols from WWTPs.},
}
@article {pmid39168387,
year = {2024},
author = {K Benny, C and Chakraborty, S},
title = {Mechanistic investigation of azo dye removal from carbon-deficient dyeing wastewater using horizontal-vertical constructed wetlands.},
journal = {Chemosphere},
volume = {364},
number = {},
pages = {143148},
doi = {10.1016/j.chemosphere.2024.143148},
pmid = {39168387},
issn = {1879-1298},
abstract = {Azo dye degradation can be achieved by simulating a series of anaerobic and aerobic conditions within the constructed wetland (CW) system. The current investigation evaluated the effectiveness of a baffled horizontal-vertical CW system, planted with Typha angustifolia, simulating anaerobic-aerobic conditions to treat carbon-deficient synthetic dyeing wastewater containing 100 mg/L Reactive Yellow 145 (RY145) azo dye. In the absence of an available carbon source in dyeing wastewater, an optimum quantity of sodium acetate was supplemented as the substrate for microbial degradation of RY145. Influent dyeing wastewater characteristics were 5555 ADMI colour, 461 mg/L chemical oxygen demand (COD) and 39 mg/L total nitrogen (TN). During the operation period, the CW system achieved 97% colour, 87% COD, 95% ammonium nitrogen (NH4[+]-N) and 71% TN removals at 4 d hydraulic retention time (HRT). Favourable environmental conditions, such as low redox conditions and substrate availability in horizontal CW, contributed to a significant reduction in colour (96%). Most TN reduction (67%) happened in horizontal CW by denitrification and plant assimilation. The metagenomic study revealed that Proteobacteria, Bacteroidetes, Chloroflexi and Firmicutes were responsible for pollutant degradation within horizontal CW. The UV-visible spectra and high-resolution liquid chromatograph mass spectrometer (HR-LCMS) analysis confirmed that dye degradation intermediates generated from the breakage of azo bonds were eliminated in vertical CW with high redox conditions. The results of the phytotoxicity and fish toxicity experiments demonstrated a substantial toxicity reduction in the CW system-treated effluent.},
}
@article {pmid39168346,
year = {2024},
author = {Li, J and Li, C and Han, Y and Yang, J and Hu, Y and Xu, H and Zhou, Y and Zuo, J and Tang, Y and Lei, C and Li, C and Wang, H},
title = {Bacterial membrane vesicles from swine farm microbial communities harboring and safeguarding diverse functional genes promoting horizontal gene transfer.},
journal = {The Science of the total environment},
volume = {951},
number = {},
pages = {175639},
doi = {10.1016/j.scitotenv.2024.175639},
pmid = {39168346},
issn = {1879-1026},
mesh = {*Gene Transfer, Horizontal ; Animals ; Swine ; Farms ; Microbiota ; Bacteria/genetics ; Feces/microbiology ; Drug Resistance, Microbial/genetics ; Wastewater/microbiology ; Drug Resistance, Bacterial/genetics ; Soil Microbiology ; Genes, Bacterial ; },
abstract = {Antibiotic resistance (AMR) poses a significant global health challenge, with swine farms recognized as major reservoirs of antibiotic resistance genes (ARGs). Recently, bacterial membrane vesicles (BMVs) have emerged as novel carriers mediating horizontal gene transfer. However, little is known about the ARGs carried by BMVs in swine farm environments and their transfer potential. This study investigated the distribution, sources, and microbiological origins of BMVs in three key microbial habitats of swine farms (feces, soil, and fecal wastewater), along with the ARGs and mobile genetic elements (MGEs) they harbor. Characterization of BMVs revealed particle sizes ranging from 20 to 500 nm and concentrations from 10[8] to 10[12] particles/g, containing DNA and proteins. Metagenomic sequencing identified BMVs predominantly composed of members of the Proteobacteria phyla, including Pseudomonadaceae, Moraxellaceae, and Enterobacteriaceae, carrying diverse functional genes encompassing resistance to 14 common antibiotics and 74,340 virulence genes. Notably, multidrug resistance, tetracycline, and chloramphenicol resistance genes were particularly abundant. Furthermore, BMVs harbored various MGEs, primarily plasmids, and demonstrated the ability to protect their DNA cargo from degradation and facilitate horizontal gene transfer, including the transmission of resistance genes. In conclusion, this study reveals widespread presence of BMVs carrying ARGs and potential virulence genes in swine farm feces, soil, and fecal wastewater. These findings not only provide new insights into the role of extracellular DNA in the environment but also highlight concerns regarding the gene transfer potential mediated by BMVs and associated health risks.},
}
@article {pmid39167968,
year = {2024},
author = {Tang, A and Zhang, J and Huang, J and Deng, Y and Wang, D and Yu, P and Zhao, R and Wang, Y and Chen, Z and Zhang, T and Li, B},
title = {Decrypting the viral community in aerobic activated sludge reactors treating antibiotic production wastewater.},
journal = {Water research},
volume = {265},
number = {},
pages = {122253},
doi = {10.1016/j.watres.2024.122253},
pmid = {39167968},
issn = {1879-2448},
mesh = {*Sewage/virology ; *Bioreactors ; *Wastewater ; *Anti-Bacterial Agents ; Waste Disposal, Fluid ; Drug Resistance, Microbial/genetics ; Viruses/genetics ; },
abstract = {Viruses are the most abundant yet understudied members that may influence microbial metabolism in activated sludge treating antibiotic production wastewater. This study comprehensively investigated virome community characteristics under the selection pressure of nine types and different concentrations of antibiotics using a metagenomics approach. Of the 15,514 total viral operational taxonomic units (tOTUs) recovered, only 37.5 % were annotated. Antibiotics altered the original viral community structure in activated sludge. The proportion of some pathogenic viral families, including Herpesviridae_like, increased significantly in reactors treating erythromycin production wastewater. In total, 16.5 % of the tOTUs were associated with two or more hosts. tOTUs rarely carried antibiotic resistance genes (ARGs), and the ARG types in the tOTUs did not match the ARGs carried by the bacterial hosts. This suggests that transduction contributes little to the horizontal ARG transfer. Auxiliary metabolic genes (AMGs) were prevalent in tOTUs, and those involved in folate biosynthesis were particularly abundant, indicating their potential to mitigate antibiotic-induced host damage. This study provides comprehensive insights into the virome community in activated sludge treating antibiotic production wastewater and sheds light on the potential role of viral AMGs in mitigating antibiotic-induced stress.},
}
@article {pmid39167702,
year = {2024},
author = {Prins, FM and Hidding, IJ and Klaassen, MAY and Collij, V and Schultheiss, JPD and Uniken Venema, WTC and Bangma, A and Aardema, JB and Jansen, BH and Mares, WGN and Witteman, BJM and Festen, EAM and Dijkstra, G and Visschedijk, MC and Fidder, HH and Vich Vila, A and Oldenburg, B and Gacesa, R and Weersma, RK},
title = {Limited predictive value of the gut microbiome and metabolome for response to biological therapy in inflammatory bowel disease.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2391505},
pmid = {39167702},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; *Inflammatory Bowel Diseases/drug therapy/microbiology/metabolism ; *Metabolome/drug effects ; *Ustekinumab/therapeutic use ; Prospective Studies ; *Antibodies, Monoclonal, Humanized/therapeutic use/pharmacology ; *Feces/microbiology ; Female ; Male ; Adult ; Biological Therapy/methods ; Treatment Outcome ; Middle Aged ; Bacteria/genetics/classification/metabolism/drug effects/isolation &amp; purification ; Biomarkers/analysis/metabolism ; },
abstract = {Emerging evidence suggests the gut microbiome's potential in predicting response to biologic treatments in patients with inflammatory bowel disease (IBD). In this prospective study, we aimed to predict treatment response to vedolizumab and ustekinumab, integrating clinical data, gut microbiome profiles based on metagenomic sequencing, and untargeted fecal metabolomics. We aimed to identify predictive biomarkers and attempted to replicate microbiome-based signals from previous studies. We found that the predictive utility of the gut microbiome and fecal metabolites for treatment response was marginal compared to clinical features alone. Testing our identified microbial ratios in an external cohort reinforced the lack of predictive power of the microbiome. Additionally, we could not confirm previously published predictive signals observed in similar sized cohorts. Overall, these findings highlight the importance of external validation and larger sample sizes, to better understand the microbiome's impact on therapy outcomes in the setting of biologicals in IBD before potential clinical implementation.},
}
@article {pmid39167161,
year = {2024},
author = {Çakar, MM and Milčić, N and Andreadaki, T and Charnock, S and Fessner, WD and Blažević, ZF},
title = {Kinetic characterization of two neuraminic acid synthases and evaluation of their application potential.},
journal = {Applied microbiology and biotechnology},
volume = {108},
number = {1},
pages = {446},
pmid = {39167161},
issn = {1432-0614},
support = {956631//Horizon 2020 Framework Programme/ ; },
mesh = {Kinetics ; Hydrogen-Ion Concentration ; *Enzyme Stability ; *Neisseria meningitidis/enzymology/genetics ; Oxo-Acid-Lyases/metabolism/genetics/chemistry ; Coenzymes/metabolism ; },
abstract = {Neuraminic acid synthases are an important yet underexplored group of enzymes. Thus, in this research, we performed a detailed kinetic and stability analysis and a comparison of previously known neuraminic acid synthase from Neisseria meningitidis, and a novel enzyme, PNH5, obtained from a metagenomic library. A systematic analysis revealed a high level of similarity of PNH5 to other known neuraminic acid synthases, except for its pH optimum, which was found to be at 5.5 for the novel enzyme. This is the first reported enzyme from this family that prefers an acidic pH value. The effect of different metal cofactors on enzyme activity, i.e. Co[2+], Mn[2+] and Mg[2+], was studied systematically. The kinetics of neuraminic acid synthesis was completely elucidated, and an appropriate kinetic model was proposed. Enzyme stability study revealed that the purified enzyme exhibits changes in its structure during time as observed by differential light scattering, which cause a drop in its activity and protein concentration. The operational enzyme stability for the neuraminic acid synthase from N. meningitidis is excellent, where no activity drop was observed during the batch reactor experiments. In the case of PNH5, some activity drop was observed at higher concentration of substrates. The obtained results present a solid platform for the future application of these enzymes in the synthesis of sialic acids. KEY POINTS: • A novel neuraminic acid synthase was characterized. • The effect of cofactors on NeuS activity was elucidated. • Kinetic and stability characterization of two neuraminic acid synthases was performed.},
}
@article {pmid39166878,
year = {2024},
author = {Lu, Q and Zhu, R and Zhou, L and Zhang, R and Li, Z and Xu, P and Wang, Z and Wu, G and Ren, J and Jiao, D and Song, Y and Li, J and Wang, W and Liang, R and Ma, X and Sun, Y},
title = {Gut dysbiosis contributes to the development of Budd-Chiari syndrome through immune imbalance.},
journal = {mSystems},
volume = {9},
number = {9},
pages = {e0079424},
pmid = {39166878},
issn = {2379-5077},
support = {81870457//MOST | National Natural Science Foundation of China (NSFC)/ ; 82172944//MOST | National Natural Science Foundation of China (NSFC)/ ; 81900558//MOST | National Natural Science Foundation of China (NSFC)/ ; 232102311048//Key science and technology project s of Henan Province/ ; },
mesh = {*Dysbiosis/microbiology/immunology ; *Gastrointestinal Microbiome/physiology ; *Budd-Chiari Syndrome/immunology/microbiology/pathology ; Humans ; Animals ; Mice ; Male ; Case-Control Studies ; Female ; *Cytokines/metabolism/immunology/genetics ; Adult ; Fecal Microbiota Transplantation ; Middle Aged ; },
abstract = {UNLABELLED: Budd-Chiari syndrome (B-CS) is a rare and lethal condition characterized by hepatic venous outflow tract blockage. Gut microbiota has been linked to numerous hepatic disorders, but its significance in B-CS pathogenesis is uncertain. First, we performed a case-control study (Ncase = 140, Ncontrol = 63) to compare the fecal microbiota of B-CS and healthy individuals by metagenomics sequencing. B-CS patients' gut microbial composition and activity changed significantly, with a different metagenomic makeup, increased potentially pathogenic bacteria, including Prevotella, and disease-linked microbial function. Imbalanced cytokines in patients were demonstrated to be associated with gut dysbiosis, which led us to suspect that B-CS is associated with gut microbiota and immune dysregulation. Next, 16S ribosomal DNA sequencing on fecal microbiota transplantation (FMT) mice models examined the link between gut dysbiosis and B-CS. FMT models showed damaged liver tissues, posterior inferior vena cava, and increased Prevotella in the disturbed gut microbiota of FMT mice. Notably, B-CS-FMT impaired the morphological structure of colonic tissues and increased intestinal permeability. Furthermore, a significant increase of the same cytokines (IL-5, IL-6, IL-9, IL-10, IL-17A, IL-17F, and IL-13) and endotoxin levels in B-CS-FMT mice were observed. Our study suggested that gut microbial dysbiosis may cause B-CS through immunological dysregulation.<br><br>IMPORTANCE: This study revealed that gut microbial dysbiosis may cause Budd-Chiari syndrome (B-CS). Gut dysbiosis enhanced intestinal permeability, and toxic metabolites and imbalanced cytokines activated the immune system. Consequently, the escalation of causative factors led to their concentration in the portal vein, thereby compromising both the liver parenchyma and outflow tract. Therefore, we proposed that gut microbial dysbiosis induced immune imbalance by chronic systemic inflammation, which contributed to the B-CS development. Furthermore, Prevotella may mediate inflammation development and immune imbalance, showing potential in B-CS pathogenesis.},
}
@article {pmid39166873,
year = {2024},
author = {Kwan, S-Y and Sabotta, CM and Cruz, LR and Wong, MC and Ajami, NJ and McCormick, JB and Fisher-Hoch, SP and Beretta, L},
title = {Gut phageome in Mexican Americans: a population at high risk for metabolic dysfunction-associated steatotic liver disease and diabetes.},
journal = {mSystems},
volume = {9},
number = {9},
pages = {e0043424},
pmid = {39166873},
issn = {2379-5077},
support = {P50 CA217674/CA/NCI NIH HHS/United States ; UL1 TR000371/TR/NCATS NIH HHS/United States ; },
mesh = {Humans ; Male ; Female ; *Gastrointestinal Microbiome/genetics ; *Bacteriophages/genetics ; Middle Aged ; *Virome/genetics ; *Mexican Americans ; *Fatty Liver/genetics ; Cross-Sectional Studies ; Adult ; Diabetes Mellitus ; Feces/microbiology/virology ; Aged ; },
abstract = {Mexican Americans are disproportionally affected by metabolic dysfunction-associated steatotic liver disease (MASLD), which often co-occurs with diabetes. Despite extensive evidence on the causative role of the gut microbiome in MASLD, studies determining the involvement of the gut phageome are scarce. In this cross-sectional study, we characterized the gut phageome in Mexican Americans of South Texas by stool shotgun metagenomic sequencing of 340 subjects, concurrently screened for liver steatosis by transient elastography. Inter-individual variations in the phageome were associated with gender, country of birth, diabetes, and liver steatosis. The phage signatures for diabetes and liver steatosis were subsequently determined. Enrichment of Inoviridae was associated with both diabetes and liver steatosis. Diabetes was further associated with the enrichment of predominantly temperate Escherichia phages, some of which possessed virulence factors. Liver steatosis was associated with the depletion of Lactococcus phages r1t and BK5-T, and enrichment of the globally prevalent Crassvirales phages, including members of genus cluster IX (Burzaovirus coli, Burzaovirus faecalis) and VI (Kahnovirus oralis). The Lactococcus phages showed strong correlations and co-occurrence with Lactococcus lactis, while the Crassvirales phages, B. coli, B. faecalis, and UAG-readthrough crAss clade correlated and co-occurred with Prevotella copri. In conclusion, we identified the gut phageome signatures for two closely linked metabolic diseases with significant global burden. These phage signatures may have utility in risk modeling and disease prevention in this high-risk population, and identification of potential bacterial targets for phage therapy.IMPORTANCEPhages influence human health and disease by shaping the gut bacterial community. Using stool samples from a high-risk Mexican American population, we provide insights into the gut phageome changes associated with diabetes and liver steatosis, two closely linked metabolic diseases with significant global burden. Common to both diseases was an enrichment of Inoviridae, a group of phages that infect bacterial hosts chronically without lysis, allowing them to significantly influence bacterial growth, virulence, motility, biofilm formation, and horizontal gene transfer. Diabetes was additionally associated with the enrichment of Escherichia coli-infecting phages, some of which contained virulence factors. Liver steatosis was additionally associated with the depletion of Lactococcus lactis-infecting phages, and enrichment of Crassvirales phages, a group of virulent phages with high global prevalence and persistence across generations. These phageome signatures may have utility in risk modeling, as well as identify potential bacterial targets for phage therapy.},
}
@article {pmid39166863,
year = {2024},
author = {Cheney, C and Johnson, JD and Ste Marie, JP and Gacosta, KYM and Denlinger Drumm, NB and Jones, GD and Waite-Cusic, J and Navab-Daneshmand, T},
title = {Resolved genomes of wastewater ESBL-producing Escherichia coli and metagenomic analysis of source wastewater samples.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0071724},
doi = {10.1128/spectrum.00717-24},
pmid = {39166863},
issn = {2165-0497},
abstract = {Extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli pose a serious threat to human health because of their resistance to the most commonly prescribed antibiotics: penicillins and cephalosporins. In this study, we provide a genomic and metagenomic context for the determinant beta-lactam resistance genes of ESBL-positive E. coli isolated from various wastewater treatment utilities in Oregon, USA. Class A beta-lactamase genes on chromosomes (blaCTX-M, blaTEM) were clustered with antibiotic resistance genes associated with other classes of antibiotics (sulfonamides and aminoglycosides) along with insertional elements. ESBL genes such as blaCTX-M, blaTEM, and blaSHV were also detected on conjugable plasmids of IncF and IncI incompatibility types. One novel IncF plasmid (pSHV2A_ESBLF) was identified, which carried a multidrug resistance genotype (blaSHV-2A, aadA22, aac3, aph6, tetA, and sul1) in addition to a mer (mercury resistance) operon, colicin, and aerobactin genes. Shotgun metagenomic analysis of the ESBL-producing E. coli-originating wastewater samples showed the presence of class A beta-lactamases; however, the ESBL genes identified in the E. coli genomes were below the detection limits. Other ESBL-associated genes (i.e., blaOXA.11, blaFOX.7, and blaGES.17) were identified in the wastewater samples, and their occurrences were correlated with the core microbial genera (e.g., Paraprevotella). In the E. coli genomes and wastewater samples, tetracycline, aminoglycoside, and beta-lactam resistance determinants frequently co-occurred. The combination of whole-genome and metagenomic analysis provides a holistic description of ESBL-producing organisms and genes in wastewater systems.IMPORTANCEUsing a hybrid sequencing and assembly strategy (short- and long-read sequencing), we identified the distribution of ARGs and virulence factors harbored on plasmids and chromosomes. We further characterized plasmids' incompatibility types and the co-occurrences of ARGs and virulence factors on plasmids and chromosomes. We investigated the transferability of plasmid-mediated beta-lactams via conjugation. Finally, using shotgun metagenomic analysis of the ESBL-producing Escherichia coli-originated wastewater samples, we described the microbial community, the resistome composition, and the potential associations with plasmid-mediated beta-lactam genes and other ARGs.},
}
@article {pmid39166855,
year = {2024},
author = {Lian, J and Ma, X and Li, X and Xia, L},
title = {The environmental microbial retrieving assessment of cell-processing facilities for cell therapy in a hospital laboratory.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0125724},
doi = {10.1128/spectrum.01257-24},
pmid = {39166855},
issn = {2165-0497},
abstract = {Cell therapy represents a promising treatment modality. A critical component in the production of cell therapy products is maintaining the sterility of cell therapy clean rooms (CTCRs). This study aimed to evaluate the environmental microbial load within CTCRs. We systematically monitored microbial load in CTCRs, following established guidelines. Cultured microbial samples underwent metagenomic sequencing, and alpha and beta diversity analyses, functional annotation, and resistance gene profiling were performed using various bioinformatics tools to assess microbial diversity and function. From November 2023 to January 2024, we collected 42 environmental microbial colony samples from various sources within the CTCR and performed metagenomic sequencing on 39 samples. Alpha diversity analysis revealed no significant differences among surface, settle_plate, and airborne categories, but significant disparities within surface subgroups were revealed. Beta diversity analysis showed notable differences between surface and airborne categories and among surface subgroups. Species distribution analysis identified Bacillus as the predominant genus on surfaces. Functional annotation and resistance gene analysis indicated distinct resistance patterns, with significant variations between subgroups, such as microscopes and transfer windows, and hands and other Grade_B environments. Resistance to hydrogen peroxide was notably higher in the transfer window group. These findings highlight the importance of stringent disinfection protocols and enhanced hand hygiene to maintain sterility in CTCRs. These findings provide valuable insights for implementing effective measures to maintain cleanliness throughout CTCRs. The annotation and study of resistance genes can help rapidly identify methods to control cellular contamination under circumstances of environmental microbial pollution.IMPORTANCEMaintaining the sterility of cell therapy clean rooms (CTCRs) is crucial for the production of safe and effective cell therapy products. Our study systematically evaluated the environmental microbial load within CTCRs, revealing significant microbial diversity and distinct resistance patterns to disinfection methods. These findings underscore the need for stringent disinfection protocols and enhanced hand hygiene practices to ensure CTCR sterility. By identifying key microbial species and their resistance genes, our research provides essential insights into controlling contamination and safeguarding the production environment, ultimately contributing to the reliability and success of cell therapy treatments.},
}
@article {pmid39165919,
year = {2024},
author = {Liu, Y and Wu, W and Xiao, Y and Zou, H and Hao, S and Jiang, Y},
title = {Application of metagenomic next-generation sequencing and targeted metagenomic next-generation sequencing in diagnosing pulmonary infections in immunocompetent and immunocompromised patients.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1439472},
pmid = {39165919},
issn = {2235-2988},
mesh = {Humans ; *Immunocompromised Host ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Male ; *Bronchoalveolar Lavage Fluid/microbiology/virology ; Female ; Middle Aged ; China ; Adult ; Aged ; Young Adult ; Bacteria/genetics/isolation &amp; purification/classification ; Sputum/microbiology/virology ; Community-Acquired Infections/diagnosis/microbiology/virology ; Adolescent ; Immunocompetence ; Pneumonia/diagnosis/microbiology/virology ; Aged, 80 and over ; },
abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) technology has been widely used to diagnose various infections. Based on the most common pathogen profiles, targeted mNGS (tNGS) using multiplex PCR has been developed to detect pathogens with predesigned primers in the panel, significantly improving sensitivity and reducing economic burden on patients. However, there are few studies on summarizing pathogen profiles of pulmonary infections in immunocompetent and immunocompromised patients in Jilin Province of China on large scale.<br><br>METHODS: From January 2021 to December 2023, bronchoalveolar lavage fluid (BALF) or sputum samples from 546 immunocompetent and immunocompromised patients with suspected community-acquired pneumonia were collected. Pathogen profiles in those patients on whom mNGS was performed were summarized. Additionally, we also evaluated the performance of tNGS in diagnosing pulmonary infections.<br><br>RESULTS: Combined with results of mNGS and culture, we found that the most common bacterial pathogens were Pseudomonas aeruginosa, Klebsiella pneumoniae, and Acinetobacter baumannii in both immunocompromised and immunocompetent patients with high detection rates of Staphylococcus aureus and Enterococcus faecium, respectively. For fungal pathogens, Pneumocystis jirovecii was commonly detected in patients, while fungal infections in immunocompetent patients were mainly caused by Candida albicans. Most of viral infections in patients were caused by Human betaherpesvirus 5 and Human gammaherpesvirus 4. It is worth noting that, compared with immunocompetent patients (34.9%, 76/218), more mixed infections were found in immunocompromised patients (37.8%, 14/37). Additionally, taking final comprehensive clinical diagnoses as reference standard, total coincidence rate of BALF tNGS (81.4%, 48/59) was much higher than that of BALF mNGS (40.0%, 112/280).<br><br>CONCLUSIONS: Our findings supplemented and classified the pathogen profiles of pulmonary infections in immunocompetent and immunocompromised patients in Jilin Province of China. Most importantly, our findings can accelerate the development and design of tNGS specifically used for regional pulmonary infections.},
}
@article {pmid39165848,
year = {2024},
author = {Xu, X and Zheng, Y and Zhang, X and Zhang, C and Gai, W and Yang, Z},
title = {Utility of Metagenomic Next-Generation Sequencing for Diagnosis of Infectious Diseases in Critically Ill Immunocompromised Pediatric Patients.},
journal = {Infection and drug resistance},
volume = {17},
number = {},
pages = {3579-3591},
pmid = {39165848},
issn = {1178-6973},
abstract = {PURPOSE: Infections cause high rates of illness and death in children worldwide. However, studies on the clinical value of metagenomic next-generation sequencing (mNGS) for immunocompromised children are still limited.<br><br>PATIENTS AND METHODS: From June 2021 to December 2023, 119 samples were collected at Pediatric Intensive Care Unit (PICU) of a single-center pediatric hospital and classified into two groups based on their immune states. We compared the diagnostic performance of mNGS and conventional microbiological test (CMT) for pathogen identification, and assessed the clinical impacts of mNGS.<br><br>RESULTS: Among the 119 samples, 48 (40.34%) belonged to the immunocompromised children. mNGS had a higher positivity rate than CMT (76.47% vs 55.46%, P = 0.0006). The positive percent agreement (PPA) of mNGS for immunocompromised children was higher compared to immunocompetent children (95.24% vs 77.78%). The most common pathogens for immunocompromised patients were gram-negative bacteria and herpesvirus. However, immunocompetent children showed a higher detection rate for gram-positive bacteria and respiratory viruses. Furthermore, the proportions of the positive impact of mNGS results were significantly higher in immunocompromised patients compared to immunocompetent patients for both diagnosis (91.67% vs 57.75%) and treatment (95.83% vs 64.79%) (P < 0.0001). Immunocompromised state, length of hospital stays, times stay in ICU, Pediatric Risk of Mortality (PRISM) score, neutrophil percentage (NEUT%) and the ratio of arterial oxygen partial pressure to fractional inspired oxygen (PaO2/FiO2) were considered independent factors for poor prognosis in critically ill pediatric patients.<br><br>CONCLUSION: In patients from PICU, mNGS had a greater clinical significance in immunocompromised children compared to immunocompetent children. mNGS technology is an important auxiliary method for achieving accurate diagnosis and treatment of critically ill pediatric patients.},
}
@article {pmid39165786,
year = {2024},
author = {Po, TL and Huang, CH and Lin, CH and Hung, HF},
title = {Diagnosis of a Rare Rickettsia felis Infection Complicated with Unusual Pericardial Effusion and Cardiac Tamponade Using an mNGS Test.},
journal = {Case reports in infectious diseases},
volume = {2024},
number = {},
pages = {8877876},
pmid = {39165786},
issn = {2090-6625},
abstract = {The occurrence of sporadic rickettsial infections has been consistently undervalued and overlooked, primarily owing to a limited emphasis on routine examinations for rickettsioses in clinical practice. At present, the immunofluorescence assay is the prevailing diagnostic method for suspected rickettsioses that enables the detection of specific antibodies against rickettsia in human serum. Herein, we present an exceptional instance of rickettsial infection that was characterized by a rare manifestation of extensive pericardial effusion leading to dyspnea and cardiac tamponade. A diagnosis of chronic fibrosing pericarditis was established based on pericardium tissue obtained through pericardiotomy, and a conclusive metagenomic next-generation sequencing test confirmed the presence of Rickettsia felis infection. The cat flea, scientifically known as Ctenocephalides felis, is the predominant carrier of R. felis. An escalating incidence of human R. felis infections has raised concerns, particularly in light of the burgeoning population of domesticated animals in many contemporary societies.},
}
@article {pmid39165569,
year = {2024},
author = {Murray, L and Fullerton, H and Moyer, CL},
title = {Microbial metabolic potential of hydrothermal vent chimneys along the submarine ring of fire.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1399422},
pmid = {39165569},
issn = {1664-302X},
abstract = {Hydrothermal vents host a diverse community of microorganisms that utilize chemical gradients from the venting fluid for their metabolisms. The venting fluid can solidify to form chimney structures that these microbes adhere to and colonize. These chimney structures are found throughout many different locations in the world's oceans. In this study, comparative metagenomic analyses of microbial communities on five chimney structures from around the Pacific Ocean were elucidated focusing on the core taxa and genes that are characteristic of each of these hydrothermal vent chimneys. The differences among the taxa and genes found at each chimney due to parameters such as physical characteristics, chemistry, and activity of the vents were highlighted. DNA from the chimneys was sequenced, assembled into contigs, and annotated for gene function. Genes used for carbon, oxygen, sulfur, nitrogen, iron, and arsenic metabolisms were found at varying abundances at each of the chimneys, largely from either Gammaproteobacteria or Campylobacteria. Many taxa shared an overlap of these functional metabolic genes, indicating that functional redundancy is critical for life at these hydrothermal vents. A high relative abundance of oxygen metabolism genes coupled with a low abundance of carbon fixation genes could be used as a unique identifier for inactive chimneys. Genes used for DNA repair, chemotaxis, and transposases were found at high abundances at each of these hydrothermal chimneys allowing for enhanced adaptations to the ever-changing chemical and physical conditions encountered.},
}
@article {pmid39165395,
year = {2024},
author = {Armbrecht, L and Bolch, CJS and Paine, B and Cooper, A and McMinn, A and Woodward, C and Hallegraeff, G},
title = {Recovering sedimentary ancient DNA of harmful dinoflagellates accumulated over the last 9000 years off Eastern Tasmania, Australia.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae098},
pmid = {39165395},
issn = {2730-6151},
abstract = {Harmful algal blooms (HABs) have had significant adverse impacts on the seafood industry along the Tasmanian east coast over the past 4 decades. To investigate the history of regional HABs, we performed analyses of sedimentary ancient DNA (sedaDNA) in coastal sediments up to ~9000 years old collected inshore and offshore of Maria Island, Tasmania. We used metagenomic shotgun sequencing and a hybridisation capture array ("HABbaits1") to target three harmful dinoflagellate genera, Alexandrium, Gymnodinium, and Noctiluca. Bioinformatic and DNA damage analyses verified the authenticity of the sedaDNA sequences. Our results show that dinoflagellates of Alexandrium genera have been present off eastern Tasmania during the last ~8300 years, and we sporadically detected and unambiguously verified sequences of Gymnodinium catenatum that were present offshore up to ~7600 years ago. We also recovered sedaDNA of the fragile, soft-bodied Noctiluca scintillans with increased relative abundance since 2010, consistent with plankton surveys. This study enabled us to identify challenges of sedaDNA sequence validation (in particular for G. catenatum, a microreticulate gymnodinoid species) and provided guidance for the development of tools to monitor past and present HAB species and improvement of future HAB event predictions.},
}
@article {pmid39165393,
year = {2024},
author = {Facimoto, CT and Clements, KD and White, WL and Handley, KM},
title = {Bacteroidia and Clostridia are equipped to degrade a cascade of polysaccharides along the hindgut of the herbivorous fish Kyphosus sydneyanus.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae102},
pmid = {39165393},
issn = {2730-6151},
abstract = {The gut microbiota of the marine herbivorous fish Kyphosus sydneyanus are thought to play an important role in host nutrition by supplying short-chain fatty acids (SCFAs) through fermentation of dietary red and brown macroalgae. Here, using 645 metagenome-assembled genomes (MAGs) from wild fish, we determined the capacity of different bacterial taxa to degrade seaweed carbohydrates along the gut. Most bacteria (99%) were unclassified at the species level. Gut communities and CAZyme-related transcriptional activity were dominated by Bacteroidia and Clostridia. Both classes possess genes CAZymes acting on internal polysaccharide bonds, suggesting their role initiating glycan depolymerization, followed by rarer Gammaproteobacteria and Verrucomicrobiae. Results indicate that Bacteroidia utilize substrates in both brown and red algae, whereas other taxa, namely, Clostridia, Bacilli, and Verrucomicrobiae, utilize mainly brown algae. Bacteroidia had the highest CAZyme gene densities overall, and Alistipes were especially enriched in CAZyme gene clusters (n = 73 versus just 62 distributed across all other taxa), pointing to an enhanced capacity for macroalgal polysaccharide utilization (e.g., alginate, laminarin, and sulfated polysaccharides). Pairwise correlations of MAG relative abundances and encoded CAZyme compositions provide evidence of potential inter-species collaborations. Co-abundant MAGs exhibited complementary degradative capacities for specific substrates, and flexibility in their capacity to source carbon (e.g., glucose- or galactose-rich glycans), possibly facilitating coexistence via niche partitioning. Results indicate the potential for collaborative microbial carbohydrate metabolism in the K. sydneyanus gut, that a greater variety of taxa contribute to the breakdown of brown versus red dietary algae, and that Bacteroidia encompass specialized macroalgae degraders.},
}
@article {pmid39165128,
year = {2024},
author = {Trost, K and Knopp, MR and Wimmer, JLE and Tria, FDK and Martin, WF},
title = {A universal and constant rate of gene content change traces pangenome flux to LUCA.},
journal = {FEMS microbiology letters},
volume = {371},
number = {},
pages = {},
pmid = {39165128},
issn = {1574-6968},
support = {101018894/ERC_/European Research Council/International ; 101018894/ERC_/European Research Council/International ; },
mesh = {*Bacteria/genetics/classification ; *Genome, Bacterial ; *Archaea/genetics/classification ; *Evolution, Molecular ; *Genome, Archaeal ; Gene Transfer, Horizontal ; Phylogeny ; },
abstract = {Prokaryotic genomes constantly undergo gene flux via lateral gene transfer, generating a pangenome structure consisting of a conserved core genome surrounded by a more variable accessory genome shell. Over time, flux generates change in genome content. Here, we measure and compare the rate of genome flux for 5655 prokaryotic genomes as a function of amino acid sequence divergence in 36 universally distributed proteins of the informational core (IC). We find a clock of gene content change. The long-term average rate of gene content flux is remarkably constant across all higher prokaryotic taxa sampled, whereby the size of the accessory genome-the proportion of the genome harboring gene content difference for genome pairs-varies across taxa. The proportion of species-level accessory genes per genome, varies from 0% (Chlamydia) to 30%-33% (Alphaproteobacteria, Gammaproteobacteria, and Clostridia). A clock-like rate of gene content change across all prokaryotic taxa sampled suggest that pangenome structure is a general feature of prokaryotic genomes and that it has been in existence since the divergence of bacteria and archaea.},
}
@article {pmid39164677,
year = {2024},
author = {Zhan, S and Li, S and Cao, Y and Liu, D and Feng, J},
title = {Value of bronchoalveolar lavage fluid metagenomic next-generation sequencing in acute exacerbation of fibrosing interstitial lung disease: an individualized treatment protocol based on microbiological evidence.},
journal = {BMC pulmonary medicine},
volume = {24},
number = {1},
pages = {400},
pmid = {39164677},
issn = {1471-2466},
support = {82300120//National Natural Science Foundation of China/ ; 82170097//National Natural Science Foundation of China/ ; },
mesh = {Humans ; Female ; *Bronchoalveolar Lavage Fluid/microbiology ; Male ; Middle Aged ; Aged ; *Lung Diseases, Interstitial/microbiology/drug therapy ; *High-Throughput Nucleotide Sequencing ; Cross-Sectional Studies ; Retrospective Studies ; Immunosuppressive Agents/administration &amp; dosage ; Metagenomics/methods ; Methylprednisolone/administration &amp; dosage ; Disease Progression ; },
abstract = {BACKGROUND: Acute exacerbation of fibrosing interstitial lung diseases (AE-ILD) is a serious life-threatening event per year. Methylprednisolone and/or immunosuppressive agents (ISA) are a mainstay in any regimen, under the premise that pulmonary infection has been promptly identified and controlled. We investigated the value of bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing (mNGS) on the treatment adjustment of AE-ILD.<br><br>METHODS: We conducted a cross-sectional observational study. All data were collected prospectively and retrospectively analyzed. We included fifty-six patients with AE-ILD and nineteen stable ILD who underwent BALF mNGS at the beginning of admission.<br><br>RESULTS: Patients with a variety of ILD classification were included. Connective-tissue disease related ILD (CTD-ILD) occupy the most common underlying non-idiopathic pulmonary fibrosis (non-IPF). The infection-triggered AE accounted for 39.29%, with the majority of cases being mixed infections. The microorganisms load in the AE-ILD group was significantly higher. After adjusted by mNGS, the therapy coverage number of pathogens was significantly higher compared to the initial treatment (p&#x2009;<&#x2009;0.001). After treatment, the GGO score and the consolidation score were significantly lower during follow up in survivors (1.57&#x2009;&#xb1;&#x2009;0.53 vs. 2.38&#x2009;&#xb1;&#x2009;0.83 with p&#x2009;<&#x2009;0.001, 1.11&#x2009;&#xb1;&#x2009;0.24 vs. 1.49&#x2009;&#xb1;&#x2009;0.47 with p&#x2009;<&#x2009;0.001, respectively). Some detected microorganisms, such as Tropheryma whipplei, Mycobacterium, Aspergillus, and mixed infections were difficult to be fully covered by empirical medication. BALF mNGS was also very helpful for excluding infections and early administration of methylprednisolone and/or ISA.<br><br>CONCLUSIONS: mNGS has been shown to be a useful tool to determine pathogens in patients with AE-ILD, the results should be fully analyzed. The comprehensive treatment protocol based on mNGS has been shown crucial in AE-ILD patients.},
}
@article {pmid39164622,
year = {2024},
author = {Dielentheis-Frenken, MRE and Wibberg, D and Blank, LM and Tiso, T},
title = {Draft genome sequence and annotation of the polyextremotolerant polyol lipid-producing fungus aureobasidium pullulans NRRL 62042.},
journal = {BMC genomic data},
volume = {25},
number = {1},
pages = {75},
pmid = {39164622},
issn = {2730-6844},
mesh = {*Genome, Fungal ; *Aureobasidium/genetics/metabolism ; *Polymers/metabolism/chemistry ; Molecular Sequence Annotation ; Lipids ; Base Composition ; },
abstract = {OBJECTIVES: The ascomycotic yeast-like fungus Aureobasidium exhibits the natural ability to synthesize several secondary metabolites, like polymalic acid, pullulan, or polyol lipids, with potential biotechnological applications. Combined with its polyextremotolerance, these properties make Aureobasidium a promising production host candidate. Hence, plenty of genomes of Aureobasidia have been sequenced recently. Here, we provide the annotated draft genome sequence of the polyol lipid-producing strain A. pullulans NRRL 62042.<br><br>DATA DESCRIPTION: The genome of A. pullulans NRRL 62042 was sequenced using Illumina NovaSeq 6000. Genome assembly revealed a genome size of 24.2&#xa0;Mb divided into 39 scaffolds with a GC content of 50.1%. Genome annotation using Genemark v4.68 and GenDBE yielded 9,596 genes.},
}
@article {pmid39164259,
year = {2024},
author = {Seong, HJ and Kim, JJ and Kim, T and Ahn, SJ and Rho, M and Lee, KJ and Sul, WJ},
title = {Recovery of 240 metagenome-assembled genomes from coastal mariculture environments in South Korea.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {902},
pmid = {39164259},
issn = {2052-4463},
mesh = {Republic of Korea ; *Metagenome ; *Aquaculture ; Animals ; Bacteria/genetics/classification ; Microbiota ; Ostreidae/microbiology ; Archaea/genetics ; Pectinidae/microbiology/genetics ; Penaeidae/microbiology/genetics ; },
abstract = {The mariculture industry has seen a rapid expansion in recent years due to the increasing global demand for seafood. However, the industry faces challenges from climate change and increased pathogen pressure. Additionally, the chemicals used to enhance mariculture productivity are changing ocean ecosystems. This study analyzed 36 surface-water metagenomes from South Korean mussel, oyster, scallop, and shrimp farms to expand our understanding of aquaculture microbial genetic resources and the potential impacts of these anthropogenic inputs. We recovered 240 non-redundant species-level metagenome-assembled genomes (MAGs), comprising 224 bacteria, 13 archaea, and three eukaryotes. Most MAGs were assigned to Proteobacteria, Bacteroidota, and Actinobacteriota, with 40.7% remaining unclassified at the species level. Among the three eukaryotic MAGs, one was identified as a novel lineage of green algae, highlighting the uncharacterized genetic diversity in mariculture environments. Additionally, 22 prokaryotic MAGs harbored 26 antibiotic and metal resistance genes, with MAGs carrying beta-lactamases being particularly prevalent in most farms. The obtained microbiome data from mariculture environments can be utilized in future studies to foster healthy, sustainable mariculture practices.},
}
@article {pmid39163860,
year = {2024},
author = {Torres, MDT and Brooks, EF and Cesaro, A and Sberro, H and Gill, MO and Nicolaou, C and Bhatt, AS and de la Fuente-Nunez, C},
title = {Mining human microbiomes reveals an untapped source of peptide antibiotics.},
journal = {Cell},
volume = {187},
number = {19},
pages = {5453-5467.e15},
doi = {10.1016/j.cell.2024.07.027},
pmid = {39163860},
issn = {1097-4172},
mesh = {Humans ; Animals ; Mice ; *Anti-Bacterial Agents/pharmacology ; *Microbiota/drug effects ; *Antimicrobial Peptides/pharmacology/chemistry ; Metagenome ; Female ; Open Reading Frames ; Bacteria/drug effects/genetics/classification ; Prevotella/drug effects ; },
abstract = {Drug-resistant bacteria are outpacing traditional antibiotic discovery efforts. Here, we computationally screened 444,054 previously reported putative small protein families from 1,773 human metagenomes for antimicrobial properties, identifying 323 candidates encoded in small open reading frames (smORFs). To test our computational predictions, 78 peptides were synthesized and screened for antimicrobial activity in vitro, with 70.5% displaying antimicrobial activity. As these compounds were different compared with previously reported antimicrobial peptides, we termed them smORF-encoded peptides (SEPs). SEPs killed bacteria by targeting their membrane, synergizing with each other, and modulating gut commensals, indicating a potential role in reconfiguring microbiome communities in addition to counteracting pathogens. The lead candidates were anti-infective in both murine skin abscess and deep thigh infection models. Notably, prevotellin-2 from Prevotella copri presented activity comparable to the commonly used antibiotic polymyxin B. Our report supports the existence of hundreds of antimicrobials in the human microbiome amenable to clinical translation.},
}
@article {pmid39163656,
year = {2024},
author = {Sun, F and Yang, H and Zhang, X and Tan, F and Wang, G and Shi, Q},
title = {Significant response of coral-associated bacteria and their carbohydrate-active enzymes diversity to coral bleaching.},
journal = {Marine environmental research},
volume = {201},
number = {},
pages = {106694},
doi = {10.1016/j.marenvres.2024.106694},
pmid = {39163656},
issn = {1879-0291},
mesh = {Animals ; *Anthozoa/microbiology ; *Bacteria/genetics/enzymology ; Symbiosis ; Microbiota ; },
abstract = {Analysis of bacterial carbohydrate-active enzymes (CAZymes) contributes significantly to comprehending the response exhibited by coral symbionts to the external environment. This study explored the impact of bleaching on the bacteria and their CAZymes in coral Favites sp. through metagenomic sequencing. Notably, principal coordinates analysis (PCoA) unveiles substantial difference in bacterial communities between bleached and unbleached corals. Proteobacteria, Actinobacteria, Acidobacteria, Bacteroidota, and Chloroflexi, exhibit noteworthy alterations during coral bleaching. CAZymes profiles in bleached coral disclosed a significant increase in Glycosyltransferases (GTs) abundance, suggesting an intensified biosynthesis of polysaccharides. Conversely, there is a marked reduction in other CAZymes abundance in bleached coral. Proteobacteria, Bacteroidota, Chlorobi, and Planctomycetota exhibit greater contributions to CAZymes in bleached corals, with Rhodobacterales, Cytophagales, Burkholderiales, Caulobacterales, and Hyphomicrobiales being the main contributors. While Acidobacteria, Actinobacteria, and Chloroflexi demonstrate higher contributions to CAZymes in unbleached corals. The changes in bacteria and their CAZymes reflect the ecological adaptability of coral holobionts when facing environmental stress. The alterations in CAZymes composition caused by bleaching events may have profound impacts on coral nutrient absorption and ecosystem stability. Therefore, understanding the dynamic changes in CAZymes is crucial for assessing the health and recovery potential of coral ecosystems.},
}
@article {pmid39163484,
year = {2024},
author = {Dede, B and Reeves, EP and Walter, M and Bach, W and Amann, R and Meyerdierks, A},
title = {Bacterial chemolithoautotrophy in ultramafic plumes along the Mid-Atlantic Ridge.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {39163484},
issn = {1751-7370},
support = {EXC-309-49926684//Deutsche Forschungsgemeinschaft/ ; //Norwegian Research Council/ ; 179560//University of Bergen Centre for Geobiology/ ; //Max Planck Society/ ; },
mesh = {*Hydrothermal Vents/microbiology ; Atlantic Ocean ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation &amp; purification ; *Chemoautotrophic Growth ; *Seawater/microbiology ; Microbiota ; Hydrogen/metabolism ; Phylogeny ; Sulfur/metabolism ; Oxidation-Reduction ; In Situ Hybridization, Fluorescence ; Carbon Dioxide/metabolism ; },
abstract = {Hydrothermal vent systems release reduced chemical compounds that act as an important energy source in the deep sea. Chemolithoautotrophic microbes inhabiting hydrothermal plumes oxidize these compounds, in particular, hydrogen and reduced sulfur, to obtain the energy required for CO2 fixation. Here, we analysed the planktonic communities of four hydrothermal systems located along the Mid-Atlantic Ridge: Irinovskoe, Semenov-2, Logatchev-1, and Ashadze-2, by combining long-read 16S rRNA gene analysis, fluorescence in situ hybridization, meta-omics, and thermodynamic calculations. Sulfurimonas and SUP05 dominated the microbial communities in these hydrothermal plumes. Investigation of Sulfurimonas and SUP05 MAGs, and their gene transcription in plumes indicated a niche partitioning driven by hydrogen and sulfur. In addition to sulfur and hydrogen oxidation, a novel SAR202 clade inhabiting the plume, here referred to as genus Carboxydicoccus, harbours the capability for CO oxidation and CO2 fixation via reverse TCA cycle. Both pathways were also highly transcribed in other hydrogen-rich plumes, including the Von Damm vent field. Carboxydicoccus profundi reached up to 4% relative abundance (1.0 x 103 cell ml- 1) in Irinovskoe non-buoyant plume and was also abundant in non-hydrothermally influenced deep-sea metagenomes (up to 5 RPKM). Therefore, CO, which is probably not sourced from the hydrothermal fluids (1.9-5.8 μM), but rather from biological activities within the rising fluid, may serve as a significant energy source in hydrothermal plumes. Taken together, this study sheds light on the chemolithoautotrophic potential of the bacterial community in Mid-Atlantic Ridge plumes.},
}
@article {pmid39162848,
year = {2024},
author = {Cupples, AM},
title = {Propane Monooxygenases in Soil Associated Metagenomes Align Most Closely to those in the Genera Kribbella, Amycolatopsis, Bradyrhizobium, Paraburkholderia and Burkholderia.},
journal = {Current microbiology},
volume = {81},
number = {10},
pages = {314},
pmid = {39162848},
issn = {1432-0991},
support = {2129228//National Science Foundation/ ; },
mesh = {*Soil Microbiology ; *Phylogeny ; *Metagenome ; Multigene Family ; Cytochrome P-450 CYP4A/genetics/metabolism ; Burkholderia/genetics/classification/enzymology ; Bradyrhizobium/genetics/classification/enzymology ; Bacterial Proteins/genetics/metabolism ; Genome, Bacterial ; },
abstract = {Propanotrophs are a focus of interest because of their ability to degrade numerous environmental contaminants. To explore the phylogeny of microorganisms containing the propane monooxygenase gene cluster (prmABCD), NCBI bacterial genomes and publicly available soil associated metagenomes (from soils, rhizospheres, tree roots) were both examined. Nucleic acid sequences were collected only if all four subunits were located together, were of the expected length and were annotated as propane monooxygenase subunits. In the bacterial genomes, this resulted in data collection only from the phyla Actinomycetota and Pseudomonadota. For the soil associated metagenomes, reads from four studies were subject to quality control, assembly and annotation. Following this, the propane monooxygenase subunit nucleic acid sequences were collected and aligned to the collected bacterial sequences. In total, forty-two propane monooxygenase gene clusters were annotated from the soil associated metagenomes. The majority aligned closely to those from the Actinomycetota, followed by the Alphaproteobacteria, then the Betaproteobacteria. Actinomycetota aligning propane monooxygenase sequences were obtained from all four datasets and most closely aligned to the genera Kribbella and Amycolatopsis. Alphaproteobacteria aligning sequences largely originated from metagenomes associated with miscanthus and switchgrass rhizospheres and primarily aligned with the genera Bradyrhizobium, Acidiphilium and unclassified Rhizobiales. Betaproteobacteria aligning sequences were obtained from only the Red Oak root metagenomes and primarily aligned with the genera Paraburkholderia, Burkholderia and Caballeronia. Interestingly, sequences from the environmental metagenomes were not closely aligned to those from well-studied propanotrophs, such as Mycobacterium and Rhodococcus. Overall, the study highlights the previously unreported diversity of putative propanotrophs in environmental samples. The common occurrence of propane monooxygenase gene clusters has implications for their potential use for contaminant biodegradation.},
}
@article {pmid39162547,
year = {2024},
author = {Jin, M and Yu, M and Feng, X and Li, Y and Zhang, M},
title = {Characterization and comparative genomic analysis of a marine Bacillus phage reveal a novel viral genus.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0003724},
doi = {10.1128/spectrum.00037-24},
pmid = {39162547},
issn = {2165-0497},
abstract = {UNLABELLED: Bacillus pumilus exhibits substantial economic significance, with its metabolism, adaptability, and ecological functions regulated by its bacteriophages. Here, we isolated and characterized a novel temperate phage vB_BpuM-ZY1 from B. pumilus derived from mangrove sediments by mitomycin C induction. Phage vB_BpuM-ZY1 is a typical myophage, which has an icosahedral head with a diameter of 43.34 ± 2.14 nm and a long contractible tail with a length of 238.58 ± 5.18 nm. Genomic analysis indicated that vB_BpuM-ZY1 encodes genes for lysogeny control, and its life cycle may be intricately regulated by multiple mechanisms. vB_BpuM-ZY1 was predicted to employ P2-like 5'-extended-cos packaging strategy. In addition, genome-wide phylogenetic tree and proteome tree analyses indicated that vB_BpuM-ZY1 belongs to the Peduoviridae family but forms a separate branch at a deeper taxonomic level. Particularly, the comparative genomic analysis showed that vB_BpuM-ZY1 has less than 70% intergenomic similarities with its most similar phages. Thus, we propose that vB_BpuM-ZY1 is a novel Bacillus phage belonging to a new genus under the Peduoviridae family. The protein-sharing network analysis identified 44 vB_BpuM-ZY1-related phages. Interestingly, these evolutionarily related myophages infect a broad range of hosts across different phyla, which may be explained by the high structural variations of the host recognition domain in their central spike proteins. Collectively, our study will contribute to our understanding of Bacillus phage diversity and Bacillus-phage interactions, as well as provide essential knowledge for the industrial application of B. pumilus.<br><br>IMPORTANCE: Although recent metagenomics research has obtained a wealth of phage genetic information, much of it is considered "dark matter" because of the lack of similarity with known sequences in the database. Therefore, the isolation and characterization of novel phages will help to interpret the vast unknown viral metagenome data and improve our understanding of phage diversity and phage-host interactions. Bacillus pumilus shows high economic relevance due to its wide applications in biotechnology, industry, biopharma, and environmental sectors. Since phages influence the abundance, metabolism, evolution, fitness, and ecological functions of bacteria through complex interactions, the significance of isolation and characterization of novel phages infecting B. pumilus is apparent. In this study, we isolated and characterized a B. pumilus phage belonging to a novel viral genus, which provides essential knowledge for phage biology as well as the industrial application of B. pumilus.},
}
@article {pmid39162524,
year = {2024},
author = {Hu, F and Cheng, Y and Fan, B and Li, W and Ye, B and Wu, Z and Tan, Z and He, Z},
title = {Ruminal microbial metagenomes and host transcriptomes shed light on individual variability in the growth rate of lambs before weaning: the regulated mechanism and potential long-term effect on the host.},
journal = {mSystems},
volume = {9},
number = {9},
pages = {e0087324},
pmid = {39162524},
issn = {2379-5077},
support = {XDA26040304, XDA26050102//strategic priority research program/ ; 32072760//MOST | National Natural Science Foundation of China (NSFC)/ ; 2022JJ10054//HSTD | Natural Science Foundation of Hunan Province/ ; 2022JBGS0023//the Inner Mongolia major technology project/ ; 2019RS3021//Innovation province project/ ; },
mesh = {Animals ; *Weaning ; Sheep/growth &amp; development/microbiology ; *Rumen/microbiology/metabolism ; *Transcriptome ; *Metagenome ; Female ; Gastrointestinal Microbiome/physiology ; Amino Acids/metabolism/blood ; Liver/metabolism ; Fermentation ; },
abstract = {UNLABELLED: Weaning weight is a reflection of management during the breastfeeding phase and will influence animal performance in subsequent phases, considered important indicators within production systems. The aims of this study were as follows: (i) to investigate variability in the growth rate among individual lambs from ewes rearing single or twin lambs fed with two different diets and (ii) to explore the molecular mechanisms regulating the growth rate and the potential long-term effects on the host. No significant change in lamb average daily gain (ADG) was observed in litter size and diet treatment, and there were large variations among individual lambs (ranging from 0.13 to 0.41 kg/day). Further analysis was conducted on serum amino acids, rumen fermentation characteristics, rumen metagenomics and transcriptome, and hepatic transcriptome of lambs with extremely high (HA; n = 6) and low (LA; n = 6) ADG. We observed significant increases in serum lysine, leucine, alanine, and phenylalanine in the HA group. The metagenome revealed that the HA group presented a higher rumen propionate molar proportion via increasing gene abundance in the succinate pathway for propionate synthesis. For the rumen transcriptome, higher expressed gene sets in the HA group were mainly related to rumen epithelial growth, including cytokine-cytokine receptor interaction, Jak-STAT signaling pathway, and adherens junction. For the liver transcriptome, the upregulated KEGG pathways in the HA group were primarily associated with fatty acid degradation, glyoxylate and dicarboxylate metabolism, cholesterol metabolism, and the immune system. This research suggests that preweaning lambs with high ADG may benefit from rumen development and enhanced liver metabolic and immune function.<br><br>IMPORTANCE: There is accumulating evidence indicating that the early-life rumen microbiome plays vital roles in rumen development and microbial fermentation, which subsequently affects the growth of young ruminants. The liver is also vital to regulate the metabolism and distribution of nutrients. Our results demonstrate that lambs with high average daily gain (ADG) enhanced microbial volatile fatty acid (VFA) metabolism toward rumen propionate and serum amino acid (AA) production to support host growth. The study highlights that high ADG in the preweaning period is beneficial for the rumen development and liver energy metabolism, leading to better growth later in life. Overall, this study explores the molecular mechanisms regulating the growth rate and the potential long-term effects of increased growth rate on the host metabolism, providing fundamental knowledge about nutrient manipulation in pre-weaning.},
}
@article {pmid39162518,
year = {2024},
author = {Hu, D and Zhang, T and He, S and Pu, T and Yin, Y and Hu, Y},
title = {Mining metagenomic data to gain a new insight into the gut microbial biosynthetic potential in placental mammals.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0086424},
doi = {10.1128/spectrum.00864-24},
pmid = {39162518},
issn = {2165-0497},
abstract = {Mammals host a remarkable diversity and abundance of gut microbes. Biosynthetic gene clusters (BGCs) in microbial genomes encode biologically active chemical products and play an important role in microbe-host interactions. Traditionally, the exploration of gut microbial metabolic functions has relied on the pure culture method. However, given the limited amounts of microbes being cultivated, insights into the metabolism of gut microbes in mammals continued to be very limited. In this study, we adopted a computational pipeline for mining the metagenomic data (named taxonomy-guided identification of biosynthetic gene clusters, TaxiBGC) to identify experimentally verified BGCs in 373 metagenomes across 53 mammalian species in an unbiased manner. We demonstrated that polyketides (PKs) and nonribosomal peptides (NRPs) are representative of mammals, and the products derived from them were associated with cell-cell communication and resistance to inflammation. Large carnivores had the highest number of BGCs, followed by large herbivores and small mammals. We also observed that the large mammals had more common BGCs that aid in the biosynthesis of a variety of natural products. However, small mammals not only had fewer BGCs but were also unique to each species. Our results provide novel insights into the mining of metagenomic data sets to identify active BGCs and their products across mammals.IMPORTANCEThe gut microbes host numerous biosynthetic gene clusters (BGCs) that biosynthesize natural products and impact the host's physiology. Historically, our understanding of BGCs in mammalian gut microbes was largely based on studies on cultured isolates; however, only a small fraction of mammal-associated microbes have been investigated. The biochemical diversity of the mammalian gut microbiota is poorly understood. Metagenomic sequencing contains data from a vast number of organisms and provides information on the total gene content of communities. Unfortunately, the existing BGC prediction tools are designed for individual microbial genomes. Recently, a BGC prediction tool called the taxonomy-guided identification of biosynthetic gene clusters (TaxiBGC) that directly mine the metagenome was developed. To gain new insights into the microbial metabolism, we used TaxiBGC to predict BGCs from 373 metagenomes across 53 mammalian species representing seven orders. Our findings elucidate the functional activities of complex microbial communities in the gut.},
}
@article {pmid39162509,
year = {2024},
author = {Liu, L and Hakhverdyan, M and Wallgren, P and Vanneste, K and Fu, Q and Lucas, P and Blanchard, Y and de Graaf, M and Oude Munnink, BB and van Boheemen, S and Bossers, A and Hulst, M and Van Borm, S},
title = {An interlaboratory proficiency test using metagenomic sequencing as a diagnostic tool for the detection of RNA viruses in swine fecal material.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0420823},
doi = {10.1128/spectrum.04208-23},
pmid = {39162509},
issn = {2165-0497},
abstract = {UNLABELLED: Metagenomic shotgun sequencing (mNGS) can serve as a generic molecular diagnostic tool. An mNGS proficiency test (PT) was performed in six European veterinary and public health laboratories to detect porcine astroviruses in fecal material and the extracted RNA. While different mNGS workflows for the generation of mNGS data were used in the different laboratories, the bioinformatic analysis was standardized using a metagenomic read classifier as well as read mapping to selected astroviral reference genomes to assess the semiquantitative representation of astrovirus species mixtures. All participants successfully identified and classified most of the viral reads to the two dominant species. The normalized read counts obtained by aligning reads to astrovirus reference genomes by Bowtie2 were in line with Kraken read classification counts. Moreover, participants performed well in terms of repeatability when the fecal sample was tested in duplicate. However, the normalized read counts per detected astrovirus species differed substantially between participants, which was related to the different laboratory methods used for data generation. Further modeling of the mNGS data indicated the importance of selecting appropriate reference data for mNGS read classification. As virus- or sample-specific biases may apply, caution is needed when extrapolating this swine feces-based PT for the detection of other RNA viruses or using different sample types. The suitability of experimental design to a given pathogen/sample matrix combination, quality assurance, interpretation, and follow-up investigation remain critical factors for the diagnostic interpretation of mNGS results.<br><br>IMPORTANCE: Metagenomic shotgun sequencing (mNGS) is a generic molecular diagnostic method, involving laboratory preparation of samples, sequencing, bioinformatic analysis of millions of short sequences, and interpretation of the results. In this paper, we investigated the performance of mNGS on the detection of porcine astroviruses, a model for RNA viruses in a pig fecal material, among six European veterinary and public health laboratories. We showed that different methods for data generation affect mNGS performance among participants and that the selection of reference genomes is crucial for read classification. Follow-up investigation remains a critical factor for the diagnostic interpretation of mNGS results. The paper contributes to potential improvements of mNGS as a diagnostic tool in clinical settings.},
}
@article {pmid39162465,
year = {2024},
author = {Chen, Z and Grim, CJ and Ramachandran, P and Meng, J},
title = {Oxford Nanopore long read-based shotgun metagenomic data sets of simulated bacterial communities originating from fresh spinach and surface water.},
journal = {Microbiology resource announcements},
volume = {13},
number = {9},
pages = {e0058624},
pmid = {39162465},
issn = {2576-098X},
abstract = {Oxford Nanopore long reads of simulated bacterial communities from fresh spinach and surface water were generated (R9.4.1+SQK-LSK109 and R10.4+SQK-LSK112; 0.5, one, and two million reads). Salmonella enterica serotype Heidelberg, Montevideo, or Typhimurium was included alone or in combination in the spinach community, while the water community harbored Pseudomonas aeruginosa.},
}
@article {pmid39162437,
year = {2024},
author = {Shean, RC and Garrett, E and Malleis, J and Lieberman, JA and Bradley, BT},
title = {A retrospective observational study of mNGS test utilization to examine the role of diagnostic stewardship at two academic medical centers.},
journal = {Journal of clinical microbiology},
volume = {62},
number = {9},
pages = {e0060524},
pmid = {39162437},
issn = {1098-660X},
mesh = {Humans ; Retrospective Studies ; *Academic Medical Centers ; *High-Throughput Nucleotide Sequencing ; Metagenomics/methods ; Antimicrobial Stewardship ; Utah ; Anti-Bacterial Agents/therapeutic use/pharmacology ; },
abstract = {UNLABELLED: Given the cost and unclear clinical impact of metagenomic next-generation sequencing (mNGS), laboratory stewardship may improve utilization. This retrospective observational study examines mNGS results from two academic medical centers employing different stewardship approaches. Eighty mNGS orders [54 cerebrospinal fluid (CSF) and 26 plasma] were identified from 2019 to 2021 at the University of Washington (UW), which requires director-level approval for mNGS orders, and the University of Utah (Utah), which does not restrict ordering. The impact of mNGS results and the relationship to traditional microbiology orders were evaluated. Nineteen percent (10/54) of CSF and 65% (17/26) of plasma studies detected at least one organism. Compared to CSF results, plasma results more frequently identified clinically significant organisms (31% vs 7%) and pathogens not detected by traditional methods (12% vs 0%). Antibiotic management was more frequently impacted by plasma versus CSF results (31% vs 4%). These outcome measures were not statistically different between study sites. The number and cumulative cost of traditional microbiology tests at UW were greater than Utah for CSF mNGS testing (UW: 46 tests, $6,237; Utah: 26 tests, $2,812; P < 0.05) but similar for plasma mNGS (UW: 31 tests, $3,975; Utah: 21 tests, $2,715; P = 0.14). mNGS testing accounted for 30%-50% of the total microbiology costs. Improving the diagnostic performance of mNGS by stewardship remains challenging due to low positivity rates and difficulties assessing clinical impact. From a fiscal perspective, stewardship efforts should focus on reducing testing in low-yield populations given the high costs of mNGS relative to overall microbiology testing expenditures.<br><br>IMPORTANCE: Metagenomic next-generation sequencing (mNGS) stewardship practices remain poorly standardized. This study aims to provide actionable insights for institutions that seek to reduce the unnecessary usage of mNGS. Importantly, we highlight that clinical impact remains challenging to measure without standardized guidelines, and we provide an actual cost estimate of microbiology expenditures on individuals undergoing mNGS.},
}
@article {pmid39161470,
year = {2024},
author = {Ye, D and Li, Y and Yan, K and Peng, W},
title = {A Case Study of Severe Pneumonia Caused by mixed Infection of Chlamydia Abortus and Influenza a in a Female Patient.},
journal = {Infection and drug resistance},
volume = {17},
number = {},
pages = {3561-3567},
pmid = {39161470},
issn = {1178-6973},
abstract = {BACKGROUND: Chlamydia abortus is a zoonotic pathogen that causes miscarriage, stillbirth, and sepsis of pregnancy in pregnant women when it infects humans. However, it rarely causes pneumonia in humans.<br><br>CASE PRESENTATION: This case reports a case of severe pneumonia characterized by high fever and cough, and the disease rapidly progressed to dyspnea. The patient was treated with moxifloxacin and doxycycline. Chlamydia abortus was detected in bronchoscopy examination and bronchoalveolar lavage fluid (BALF) through metagenomic next-generation sequencing (mNGS)-DNA. A weak positive for influenza A (H1N1) antigen was also found in the throat swab tested. Subsequently, we added mabaloxavir and replaced doxycycline with an intravenous infusion of omadacycline. After effective treatment, the patient developed a urinary tract infection, and the treatment plan was adjusted to meropenem combined with omadacycline. The patient's condition improved, and she was discharged on the 14th day of admission.<br><br>CONCLUSION: This is the first report of cases of non-pregnant female patients with Chlamydia abortus infection pneumonia. Consequently, infections with Chlamydia abortus can result in severe respiratory distress, disturbance of water and electrolyte balance, and abnormal liver function, which requires timely diagnosis and correct use of antibiotics by clinicians. Consequently, the mixed infection of H1N1 and Chlamydia abortus aggravated the complexity of the condition and treatment. Combining tetracycline and quinolone is effective for treating severe pneumonia with Chlamydia abortus infection.},
}
@article {pmid39161223,
year = {2024},
author = {Stokholm, J and Thorsen, J and Schoos, AM and Rasmussen, MA and Brandt, S and Sørensen, SJ and Vahman, N and Chawes, B and Bønnelykke, K},
title = {Infantile colic is associated with development of later constipation and atopic disorders.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.16274},
pmid = {39161223},
issn = {1398-9995},
support = {//Region Hovedstaden/ ; //Strategiske Forskningsr&#xe5;d/ ; //Lundbeck Foundation/ ; //Sundhed og Sygdom, Det Frie Forskningsr&#xe5;d/ ; },
abstract = {BACKGROUND: Infantile colic is a common condition with limited knowledge about later clinical manifestations. We evaluated the role of the early life gut microbiome in infantile colic and later development of atopic and gastrointestinal disorders.<br><br>METHODS: Copenhagen Prospective Studies on Asthma in Childhood2010 cohort was followed with 6&#x2009;years of extensive clinical phenotyping. The 1-month gut microbiome was analyzed by 16S rRNA sequencing. Infantile colic was evaluated at age 3&#x2009;months by interviews. Clinical endpoints included constipation to age 3&#x2009;years and prospectively diagnosed asthma and atopic dermatitis in the first 6&#x2009;years of life, and allergic sensitization from skin prick tests, specific Immunoglobulin E, and component analyses.<br><br>RESULTS: Of 695 children, 55 children (7.9%) had infantile colic. Several factors were associated with colic including race, breastfeeding, and pets. The 1-month gut microbiome composition and taxa abundances were not associated with colic, however a sparse Partial Least Squares model including combined abundances of nine species was moderately predictive of colic: median, cross-validated AUC&#x2009;=&#x2009;0.627, p&#x2009;=&#x2009;.003. Children with infantile colic had an increased risk of developing constipation (aOR, 2.88 [1.51-5.35], p&#x2009;=&#x2009;.001) later in life, but also asthma (aHR, 1.69 [1.02-2.79], p&#x2009;=&#x2009;.040), atopic dermatitis (aHR, 1.84 [1.20-2.81], p&#x2009;=&#x2009;.005) and had a higher number of positive allergic components (adjusted difference, 116% [14%-280%], p&#x2009;=&#x2009;.012) in the first 6&#x2009;years. These associations were not mediated by gut microbiome differences.<br><br>CONCLUSIONS: We link infantile colic with risk of developing constipation and atopic disorders in the first 6&#x2009;years of life, which was not mediated through an altered gut microbiome at age 1-month. These results suggest infantile colic to involve gastrointestinal and/or atopic mechanisms.},
}
@article {pmid39160620,
year = {2024},
author = {Yu, T and Luo, Y and Tan, X and Zhao, D and Bi, X and Li, C and Zheng, Y and Xiang, H and Hu, S},
title = {Global Marine Cold Seep Metagenomes Reveal Diversity of Taxonomy, Metabolic Function, and Natural Products.},
journal = {Genomics, proteomics &amp; bioinformatics},
volume = {22},
number = {2},
pages = {},
doi = {10.1093/gpbjnl/qzad006},
pmid = {39160620},
issn = {2210-3244},
support = {//Center for Ocean Mega-Science, Chinese Academy of Sciences/ ; 2021QZKK0100//Second Tibetan Plateau Scientific Expedition and Research Program/ ; },
mesh = {*Metagenome/genetics ; *Archaea/genetics/metabolism/classification ; *Microbiota/genetics ; Bacteria/genetics/classification/metabolism ; Biological Products/metabolism ; Cold Temperature ; Phylogeny ; Seawater/microbiology ; Metagenomics/methods ; Biodiversity ; },
abstract = {Cold seeps in the deep sea are closely linked to energy exploration as well as global climate change. The alkane-dominated chemical energy-driven model makes cold seeps an oasis of deep-sea life, showcasing an unparalleled reservoir of microbial genetic diversity. Here, by analyzing 113 metagenomes collected from 14 global sites across 5 cold seep types, we present a comprehensive Cold Seep Microbiomic Database (CSMD) to archive the genomic and functional diversity of cold seep microbiomes. The CSMD includes over 49 million non-redundant genes and 3175 metagenome-assembled genomes, which represent 1895 species spanning 105 phyla. In addition, beta diversity analysis indicates that both the sampling site and cold seep type have a substantial impact on the prokaryotic microbiome community composition. Heterotrophic and anaerobic metabolisms are prevalent in microbial communities, accompanied by considerable mixotrophs and facultative anaerobes, highlighting the versatile metabolic potential in cold seeps. Furthermore, secondary metabolic gene cluster analysis indicates that at least 98.81% of the sequences potentially encode novel natural products, with ribosomally synthesized and post-translationally modified peptides being the predominant type widely distributed in archaea and bacteria. Overall, the CSMD represents a valuable resource that would enhance the understanding and utilization of global cold seep microbiomes.},
}
@article {pmid39160615,
year = {2024},
author = {Hugerth, LW and Krog, MC and Vomstein, K and Du, J and Bashir, Z and Kaldhusdal, V and Fransson, E and Engstrand, L and Nielsen, HS and Schuppe-Koistinen, I},
title = {Defining Vaginal Community Dynamics: daily microbiome transitions, the role of menstruation, bacteriophages, and bacterial genes.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {153},
pmid = {39160615},
issn = {2049-2618},
support = {KAW 2020.0239//Science for Life Laboratory/ ; E-22614-01, E-22614-02//Rigshospitalet/ ; 2021-01683//Vetenskapsr&#xe5;det/ ; },
mesh = {Humans ; Female ; *Vagina/microbiology ; *Bacteriophages/genetics/physiology ; *Microbiota/genetics ; *Menstruation ; *Bacteria/classification/genetics ; Adult ; *Dysbiosis/microbiology ; *Menstrual Cycle ; Young Adult ; Genes, Bacterial/genetics ; Metagenomics/methods ; },
abstract = {BACKGROUND: The composition of the vaginal microbiota during the menstrual cycle is dynamic, with some women remaining eu- or dysbiotic and others transitioning between these states. What defines these dynamics, and whether these differences are microbiome-intrinsic or mostly driven by the host is unknown. To address this, we characterized 49 healthy, young women by metagenomic sequencing of daily vaginal swabs during a menstrual cycle. We classified the dynamics of the vaginal microbiome and assessed the impact of host behavior as well as microbiome differences at the species, strain, gene, and phage levels.<br><br>RESULTS: Based on the daily shifts in community state types (CSTs) during a menstrual cycle, the vaginal microbiome was classified into four Vaginal Community Dynamics (VCDs) and reported in a classification tool, named VALODY: constant eubiotic, constant dysbiotic, menses-related, and unstable dysbiotic. The abundance of bacteria, phages, and bacterial gene content was compared between the four VCDs. Women with different VCDs showed significant differences in relative phage abundance and bacterial composition even when assigned to the same CST. Women with unstable VCDs had higher phage counts and were more likely dominated by L. iners. Their Gardnerella spp. strains were also more likely to harbor bacteriocin-coding genes.<br><br>CONCLUSIONS: The VCDs present a novel time series classification that highlights the complexity of varying degrees of vaginal dysbiosis. Knowing the differences in phage gene abundances and the genomic strains present allows a deeper understanding of the initiation and maintenance of permanent dysbiosis. Applying the VCDs to further characterize the different types of microbiome dynamics qualifies the investigation of disease and enables comparisons at individual and population levels. Based on our data, to be able to classify a dysbiotic sample into the accurate VCD, clinicians would need two to three mid-cycle samples and two samples during menses. In the future, it will be important to address whether transient VCDs pose a similar risk profile to persistent dysbiosis with similar clinical outcomes. This framework may aid interdisciplinary translational teams in deciphering the role of the vaginal microbiome in women's health and reproduction. Video Abstract.},
}
@article {pmid39160591,
year = {2024},
author = {Lee, H and Hwang, K and Cho, A and Kim, S and Kim, M and Morgan-Kiss, R and Priscu, JC and Kim, KM and Kim, OS},
title = {Microbial assemblages and associated biogeochemical processes in Lake Bonney, a permanently ice-covered lake in the McMurdo Dry Valleys, Antarctica.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {60},
pmid = {39160591},
issn = {2524-6372},
support = {PE23130//Korea Polar Research Institute/ ; PE23130//Korea Polar Research Institute/ ; PE23130//Korea Polar Research Institute/ ; PE23130//Korea Polar Research Institute/ ; PE23130//Korea Polar Research Institute/ ; PE23130//Korea Polar Research Institute/ ; PE23130//Korea Polar Research Institute/ ; OPP 1637708//National Science Foundation/ ; OPP 1637708//National Science Foundation/ ; },
abstract = {BACKGROUND: Lake Bonney, which is divided into a west lobe (WLB) and an east lobe (ELB), is a perennially ice-covered lake located in the McMurdo Dry Valleys of Antarctica. Despite previous reports on the microbial community dynamics of ice-covered lakes in this region, there is a paucity of information on the relationship between microbial genomic diversity and associated nutrient cycling. Here, we applied gene- and genome-centric approaches to investigate the microbial ecology and reconstruct microbial metabolic potential along the depth gradient in Lake Bonney.<br><br>RESULTS: Lake Bonney is strongly chemically stratified with three distinct redox zones, yielding different microbial niches. Our genome enabled approach revealed that in the sunlit and relatively freshwater epilimnion, oxygenic photosynthetic production by the cyanobacterium Pseudanabaena and a diversity of protists and microalgae may provide new organic carbon to the environment. CO-oxidizing bacteria, such as Acidimicrobiales, Nanopelagicales, and Burkholderiaceae were also prominent in the epilimnion and their ability to oxidize carbon monoxide to carbon dioxide may serve as a supplementary energy conservation strategy. In the more saline metalimnion of ELB, an accumulation of inorganic nitrogen and phosphorus supports photosynthesis despite relatively low light levels. Conversely, in WLB the release of organic rich subglacial discharge from Taylor Glacier into WLB would be implicated in the possible high abundance of heterotrophs supported by increased potential for glycolysis, beta-oxidation, and glycoside hydrolase and may contribute to the growth of iron reducers in the dark and extremely saline hypolimnion of WLB. The suboxic and subzero temperature zones beneath the metalimnia in both lobes supported microorganisms capable of utilizing reduced nitrogens and sulfurs as electron donors. Heterotrophs, including nitrate reducing sulfur oxidizing bacteria, such as Acidimicrobiales (MAG72) and Salinisphaeraceae (MAG109), and denitrifying bacteria, such as Gracilimonas (MAG7), Acidimicrobiales (MAG72) and Salinisphaeraceae (MAG109), dominated the hypolimnion of WLB, whereas the environmental harshness of the hypolimnion of ELB was supported by the relatively low in metabolic potential, as well as the abundance of halophile Halomonas and endospore-forming Virgibacillus.<br><br>CONCLUSIONS: The vertical distribution of microbially driven C, N and S cycling genes/pathways in Lake Bonney reveals the importance of geochemical gradients to microbial diversity and biogeochemical cycles with the vertical water column.},
}
@article {pmid39160564,
year = {2024},
author = {Chen, X and Yin, X and Shi, X and Yan, W and Yang, Y and Liu, L and Zhang, T},
title = {Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes.},
journal = {Genome biology},
volume = {25},
number = {1},
pages = {226},
pmid = {39160564},
issn = {1474-760X},
support = {T21-705/20-N//University Grants Committee/ ; },
mesh = {*Metagenomics/methods ; Metagenome ; Genetic Markers ; Wastewater/microbiology ; Software ; },
abstract = {Long-read sequencing holds great potential for characterizing complex microbial communities, yet taxonomic profiling tools designed specifically for long reads remain lacking. We introduce Melon, a novel marker-based taxonomic profiler that capitalizes on the unique attributes of long reads. Melon employs a two-stage classification scheme to reduce computational time and is equipped with an expectation-maximization-based post-correction module to handle ambiguous reads. Melon achieves superior performance compared to existing tools in both mock and simulated samples. Using wastewater metagenomic samples, we demonstrate the applicability of Melon by showing it provides reliable estimates of overall genome copies, and species-level taxonomic profiles.},
}
@article {pmid39160043,
year = {2024},
author = {Merino, N and Pagán, E and Berdejo, D and Worby, CJ and Young, M and Manson, AL and Pagán, R and Earl, AM and García-Gonzalo, D},
title = {Dynamics of microbiome and resistome in a poultry burger processing line.},
journal = {Food research international (Ottawa, Ont.)},
volume = {193},
number = {},
pages = {114842},
doi = {10.1016/j.foodres.2024.114842},
pmid = {39160043},
issn = {1873-7145},
mesh = {Animals ; *Microbiota/genetics ; *Food Microbiology ; *Bacteria/genetics/classification/isolation &amp; purification/drug effects ; *Food Handling/methods ; Poultry/microbiology ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing ; Drug Resistance, Bacterial/genetics ; Meat/microbiology ; Poultry Products/microbiology ; },
abstract = {Traditionally, surveillance programs for food products and food processing environments have focused on targeted pathogens and resistance genes. Recent advances in high throughput sequencing allow for more comprehensive and untargeted monitoring. This study assessed the microbiome and resistome in a poultry burger processing line using culturing techniques and whole metagenomic sequencing (WMS). Samples included meat, burgers, and expired burgers, and different work surfaces. Microbiome analysis revealed spoilage microorganisms as the main microbiota, with substantial shifts observed during the shelf-life period. Core microbiota of meat and burgers included Pseudomonas spp., Psychrobacter spp., Shewanella spp. and Brochothrix spp., while expired burgers were dominated by Latilactobacillus spp. and Leuconostoc spp. Cleaning and disinfection (C&amp;D) procedures altered the microbial composition of work surfaces, which still harbored Hafnia spp. and Acinetobacter spp. after C&amp;D. Resistome analysis showed a low overall abundance of resistance genes, suggesting that effective interventions during processing may mitigate their transmission. However, biocide resistance genes were frequently found, indicating potential biofilm formation or inefficient C&amp;D protocols. This study demonstrates the utility of combining culturing techniques and WMS for comprehensive of the microbiome and resistome characterization in food processing lines.},
}
@article {pmid39160038,
year = {2024},
author = {Coria-Hinojosa, LM and Velásquez-Reyes, D and Alcázar-Valle, M and Kirchmayr, MR and Calva-Estrada, S and Gschaedler, A and Mojica, L and Lugo, E},
title = {Exploring volatile compounds and microbial dynamics: Kluyveromyces marxianus and Hanseniaspora opuntiae reduce Forastero cocoa fermentation time.},
journal = {Food research international (Ottawa, Ont.)},
volume = {193},
number = {},
pages = {114821},
doi = {10.1016/j.foodres.2024.114821},
pmid = {39160038},
issn = {1873-7145},
mesh = {*Fermentation ; *Volatile Organic Compounds/analysis/metabolism ; *Kluyveromyces/metabolism ; *Hanseniaspora/metabolism ; *Cacao/microbiology/metabolism/chemistry ; Food Microbiology ; Gas Chromatography-Mass Spectrometry ; Acetic Acid/metabolism ; Time Factors ; },
abstract = {Traditional cocoa bean fermentation is a spontaneous process and can result in heterogeneous sensory quality. For this reason, yeast-integrated starter cultures may be an option for creating consistent organoleptic profiles. This study proposes the mixture of Hanseniaspora opuntiae and Kluyveromyces marxianus (from non-cocoa fermentation) as starter culture candidates. The microorganisms and volatile compounds were analyzed during the cocoa fermentation process, and the most abundant were correlated with predominant microorganisms. Results showed that Kluyveromyces marxianus, isolated from mezcal fermentation, was identified as the dominant yeast by high-throughput DNA sequencing. A total of 63 volatile compounds identified by HS-SPME-GC-MS were correlated with the more abundant bacteria and yeast using Principal Component Analysis and Agglomerative Hierarchical Clustering. This study demonstrates that yeasts from other fermentative processes can be used as starter cultures in cocoa fermentation and lead to the formation of more aromatic esters, decrease the acetic acid content.},
}
@article {pmid39159777,
year = {2024},
author = {Fang, XM and Li, J and Wang, NF and Zhang, T and Yu, LY},
title = {Metagenomics uncovers microbiome and resistome in soil and reindeer faeces from Ny-Ålesund (Svalbard, High Arctic).},
journal = {Environmental research},
volume = {262},
number = {Pt 1},
pages = {119788},
doi = {10.1016/j.envres.2024.119788},
pmid = {39159777},
issn = {1096-0953},
abstract = {Research on the microbiome and resistome in polar environments, such as the Arctic, is crucial for understanding the emergence and spread of antibiotic resistance genes (ARGs) in the environment. In this study, soil and reindeer faeces samples collected from Ny-Ålesund (Svalbard, High Arctic) were examined to analyze the microbiome, ARGs, and biocide/metal resistance genes (BMRGs). The dominant phyla in both soil and faeces were Pseudomonadota, Actinomycetota, and Bacteroidota. A total of 2618 predicted Open Reading Frames (ORFs) containing antibiotic resistance genes (ARGs) were detected. These ARGs belong to 162 different genes across 17 antibiotic classes, with rifamycin and multidrug resistance genes being the most prevalent. We focused on investigating antibiotic resistance mechanisms in the Ny-Ålesund environment by analyzing the resistance genes and their biological pathways. Procrustes analysis demonstrated a significant correlation between bacterial communities and ARG/BMRG profiles in soil and faeces samples. Correlation analysis revealed that Pseudomonadota contributed most to multidrug and triclosan resistance, while Actinomycetota were predominant contributors to rifamycin and aminoglycoside resistance. The geochemical factors, SiO4[2-] and NH4[+], were found to significantly influence the microbial composition and ARG distribution in the soil samples. Analysis of ARGs, BMRGs, virulence factors (VFs), and pathogens identified potential health risks associated with certain bacteria, such as Cryobacterium and Pseudomonas, due to the presence of different genetic elements. This study provided valuable insights into the molecular mechanisms and geochemical factors contributing to antibiotic resistance and enhanced our understanding of the evolution of antibiotic resistance genes in the environment.},
}
@article {pmid39159729,
year = {2024},
author = {Ma, J and Li, M and Bao, Y and Huang, W and He, X and Hong, Y and Wei, W and Liu, Z and Gao, X and Yang, Y and Cui, Z and Wang, W and Wang, J and Zhu, W and Zheng, N and Pan, L and Wang, D and Ke, Z and Zhou, B and Sheng, L and Li, H},
title = {Gut microbiota-brain bile acid axis orchestrates aging-related neuroinflammation and behavior impairment in mice.},
journal = {Pharmacological research},
volume = {208},
number = {},
pages = {107361},
doi = {10.1016/j.phrs.2024.107361},
pmid = {39159729},
issn = {1096-1186},
mesh = {Animals ; *Gastrointestinal Microbiome ; *Aging/metabolism ; Male ; *Bile Acids and Salts/metabolism ; *Neuroinflammatory Diseases/metabolism ; Female ; *Brain-Gut Axis/physiology ; *Mice, Inbred C57BL ; Mice ; *Brain/metabolism ; *Behavior, Animal ; Caenorhabditis elegans/microbiology ; Microglia/metabolism ; },
abstract = {Emerging evidence shows that disrupted gut microbiota-bile acid (BA) axis is critically involved in the development of neurodegenerative diseases. However, the alterations in spatial distribution of BAs among different brain regions that command important functions during aging and their exact roles in aging-related neurodegenerative diseases are poorly understood. Here, we analyzed the BA profiles in cerebral cortex, hippocampus, and hypothalamus of young and natural aging mice of both sexes. The results showed that aging altered brain BA profiles sex- and region- dependently, in which TβMCA was consistently elevated in aging mice of both sexes, particularly in the hippocampus and hypothalamus. Furthermore, we found that aging accumulated-TβMCA stimulated microglia inflammation in vitro and shortened the lifespan of C. elegans, as well as behavioral impairment and neuroinflammation in mice. In addition, metagenomic analysis suggested that the accumulation of brain TβMCA during aging was partially attributed to reduction in BSH-carrying bacteria. Finally, rejuvenation of gut microbiota by co-housing aged mice with young mice restored brain BA homeostasis and improved neurological dysfunctions in natural aging mice. In conclusion, our current study highlighted the potential of improving aging-related neuro-impairment by targeting gut microbiota-brain BA axis.},
}
@article {pmid39159726,
year = {2024},
author = {Zhang, Y and Wang, N and Wan, J and Jousset, A and Jiang, G and Wang, X and Wei, Z and Xu, Y and Shen, Q},
title = {Exploring the antibiotic resistance genes removal dynamics in chicken manure by composting.},
journal = {Bioresource technology},
volume = {410},
number = {},
pages = {131309},
doi = {10.1016/j.biortech.2024.131309},
pmid = {39159726},
issn = {1873-2976},
mesh = {Animals ; *Manure/microbiology ; *Chickens ; *Composting ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Bacteria/genetics/drug effects ; Microbiota/drug effects ; Gene Transfer, Horizontal ; },
abstract = {Prolonged antibiotic usage in livestock farming leads to the accumulation of antibiotic resistance genes in animal manure. Composting has been shown as an effective way of removing antibiotic resistance from manures, but the specific mechanisms remain unclear. This study used time-series sampling and metagenomics to analyse the resistome types and their bacterial hosts in chicken manures. Composting significantly altered the physicochemical properties and microbiome composition, reduced antibiotic resistance genes by 65.71 %, mobile genetic elements by 68.15 % and horizontal gene transfer frequency. Source tracking revealed that Firmicutes, Actinobacteria, and Proteobacteria are the major bacterial hosts involved in the resistome and gene transfer events. Composting reduces the resistome risk by targeting pathogens such as Staphylococcus aureus. Structural equation modelling confirmed that composting reduces resistome risk by changing pH and pathogen abundance. This study demonstrates that composting is an effective strategy for mitigating resistome risk in chicken manure, thereby supporting the One Health initiative.},
}
@article {pmid39159437,
year = {2024},
author = {Pozarycki, C and Seaton, KM and C Vincent, E and Novak Sanders, C and Nuñez, N and Castillo, M and Ingall, E and Klempay, B and Pontefract, A and Fisher, LA and Paris, ER and Buessecker, S and Alansson, NB and Carr, CE and Doran, PT and Bowman, JS and Schmidt, BE and Stockton, AM},
title = {Biosignature Molecules Accumulate and Persist in Evaporitic Brines: Implications for Planetary Exploration.},
journal = {Astrobiology},
volume = {24},
number = {8},
pages = {795-812},
doi = {10.1089/ast.2023.0122},
pmid = {39159437},
issn = {1557-8070},
mesh = {*Exobiology/methods ; *Extraterrestrial Environment/chemistry ; *Salts/analysis/chemistry ; Adenosine Triphosphate/analysis/metabolism ; Amino Acids/analysis ; Salinity ; Organic Chemicals/analysis ; Space Flight ; Seawater/chemistry/microbiology/analysis ; },
abstract = {The abundance of potentially habitable hypersaline environments in our solar system compels us to understand the impacts of high-salt matrices and brine dynamics on biosignature detection efforts. We identified and quantified organic compounds in brines from South Bay Salt Works (SBSW), where evapoconcentration of ocean water enables exploration of the impact of NaCl- and MgCl2-dominated brines on the detection of potential biosignature molecules. In SBSW, organic biosignature abundance and distribution are likely influenced by evapoconcentration, osmolyte accumulation, and preservation effects. Bioluminescence assays show that adenosine triphosphate (ATP) concentrations are higher in NaCl-rich, low water activity (aw) samples (<0.85) from SBSW. This is consistent with the accumulation and preservation of ATP at low aw as described in past laboratory studies. The water-soluble small organic molecule inventory was determined by using microchip capillary electrophoresis paired with high-resolution mass spectrometry (µCE-HRMS). We analyzed the relative distribution of proteinogenic amino acids with a recently developed quantitative method using CE-separation and laser-induced fluorescence (LIF) detection of amino acids in hypersaline brines. Salinity trends for dissolved free amino acids were consistent with amino acid residue abundance determined from the proteome of the microbial community predicted from metagenomic data. This highlights a tangible connection up and down the "-omics" ladder across changing geochemical conditions. The detection of water-soluble organic compounds, specifically proteinogenic amino acids at high abundance (>7 mM) in concentrated brines, demonstrates that potential organic biomarkers accumulate at hypersaline sites and suggests the possibility of long-term preservation. The detection of such molecules in high abundance when using diverse analytical tools appropriate for spacecraft suggests that life detection within hypersaline environments, such as evaporates on Mars and the surface or subsurface brines of ocean world Europa, is plausible and argues such environments should be a high priority for future exploration. Key Words: Salts-Analytical chemistry-Amino acids-Biosignatures-Capillary electrophoresis-Preservation. Astrobiology 24, 795-812.},
}
@article {pmid39159427,
year = {2024},
author = {Yagi, K and Ethridge, AD and Falkowski, NR and Huang, YJ and Elesela, S and Huffnagle, GB and Lukacs, NW and Fonseca, W and Asai, N},
title = {Microbiome modifications by steroids during viral exacerbation of asthma and in healthy mice.},
journal = {American journal of physiology. Lung cellular and molecular physiology},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajplung.00040.2024},
pmid = {39159427},
issn = {1522-1504},
support = {AI138348//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; HL150682//HHS | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; AI089473//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; },
abstract = {In the present studies the assessment of how viral exacerbation of asthmatic responses with and without pulmonary steroid treatment altered the microbiome in conjunction with immune responses presents striking data. The overall findings identify that while steroid treatment of allergic animals diminished the severity of the respiratory syncytial virus (RSV)-induced exacerbation of airway function and mucus hypersecretion, there were local increases in IL-17A expression. Analysis of lung and gut microbiome suggested that there are differences in the RSV exacerbation that are further altered by fluticasone (FLUT) treatment. Using metagenomic inference software, PICRUSt2, we were able to predict that the metabolite profile that the changed gut microbiome produced was significantly different with multiple metabolic pathways and associated with specific treatments with or without FLUT. Importantly, measuring plasma metabolites, our data indicate that there are significant changes associated with chronic allergen exposure, RSV exacerbation, and with FLUT treatment. The changes to the metabolites have contributions from both host and microbial pathways. To understand if airway steroids on their own altered lung and gut microbiome along with host responses to RSV infection, naïve animals were treated with FLUT prior to RSV infection. The naïve animals with FLUT prior to RSV infection demonstrated enhanced disease corresponding to altered microbiome and the PICRUSt2 metagenomic inference analysis. Altogether, these findings set the foundation for identifying important correlations of severe viral exacerbated allergic disease with microbiome changes a potential for early life pulmonary steroid influence on subsequent viral induced disease.},
}
@article {pmid39159233,
year = {2024},
author = {Katsumi, T and Sato, H and Murakami, R and Hanatani, T and Uchiyama, F and Suzuki, F and Maki, K and Hoshikawa, K and Haga, H and Saito, T and Ueno, Y},
title = {Identification of microbial antigens in liver tissues involved in the pathogenesis of primary biliary cholangitis using 16S rRNA metagenome analysis.},
journal = {PloS one},
volume = {19},
number = {8},
pages = {e0308912},
pmid = {39159233},
issn = {1932-6203},
mesh = {*RNA, Ribosomal, 16S/genetics ; Humans ; *Liver/microbiology/pathology ; *Liver Cirrhosis, Biliary/microbiology/genetics ; Metagenome ; Antigens, Bacterial/genetics ; Female ; Male ; Middle Aged ; Metagenomics/methods ; Bacteria/genetics/classification/isolation &amp; purification ; Aged ; },
abstract = {BACKGROUND: Multiple factors are involved in the pathogenesis of primary biliary cholangitis (PBC), a chronic cholestatic liver disease, characterized by intrahepatic cholangiopathy. In particular, studies have suggested that environmental factors such as the presence of granulomas in the portal vein region are important for the development of PBC. This study aimed to comprehensively analyze and identify foreign-derived antigens in PBC liver tissue to confirm their involvement in PBC pathogenesis.<br><br>METHODS: Portal areas and hepatocyte regions were selectively dissected from formalin-fixed paraffin-embedded PBC liver tissue samples using the microlaser method, followed by total DNA extraction. We then validated whether the bacterial strains identified through 16S rRNA metagenomic analysis were detected in PBC liver tissues.<br><br>RESULTS: The most frequently detected bacterial genera in the PBC liver tissue samples were Sphingomonas panacis, Providencia, and Cutibacterium. These bacterial genera were also detected in the other PBC samples. Validation for the detection of S. panacis, the most abundant genus, revealed polymerase chain reaction bands extracted from the portal areas of all samples. They were also more highly expressed than bands detected in the hepatocyte region.<br><br>CONCLUSION: S. panacis antigen was specifically detected in the portal areas of PBC liver tissues. The introduction of foreign-derived antigens into the liver as an environmental factor could be a possible mechanism for the development of PBC.},
}
@article {pmid39158759,
year = {2024},
author = {Li, EC and Lai, QL and Zhang, TY and Du, BQ and Zhao, J and Cai, MT and Zhang, YX and Fang, GL},
title = {Type 2 herpes simplex virus-induced anti-N-methyl-D-aspartate receptor encephalitis responsive to immunoglobulin monotherapy.},
journal = {Journal of neurovirology},
volume = {},
number = {},
pages = {},
pmid = {39158759},
issn = {1538-2443},
abstract = {Herpes simplex virus-2 encephalitis (HSV2E) in immunocompetent adults is exceptionally rare, and the subsequent onset of autoimmune encephalitis after HSV2E is even less common. This report presents the inaugural Chinese case of anti-N-methyl-D-aspartate receptor encephalitis (NMDARE) induced by HSV2E, confirmed via metagenomic next-generation sequencing (mNGS). The patient demonstrated a favorable response to intravenous immunoglobulin (IVIG) monotherapy. This case emphasizes the importance of considering autoimmune encephalitis in patients exhibiting new or recurrent neurological symptoms after HSV2E recovery. Comprehensive mNGS and neuronal antibody testing are essential for timely diagnosis. Moreover, IVIG monotherapy can serve as an effective treatment for NMDARE induced by HSV2, providing a viable alternative, particularly when steroid therapy is contraindicated.},
}
@article {pmid39158623,
year = {2024},
author = {Sankaranarayanan, G and Kodiveri Muthukaliannan, G},
title = {Deeper Exploration of Gut Microbiome: Profile of Resistome, Virome and Viral Auxiliary Metabolic Genes of Three Ethnic Indian Groups.},
journal = {Molecular biotechnology},
volume = {},
number = {},
pages = {},
pmid = {39158623},
issn = {1559-0305},
support = {AMR/Fellowship/20/2022-ECD-lI//Indian Council of Medical Research/ ; },
abstract = {The current study explored the resistomes and viromes of three Indian ethnic populations: Jaisalmer, Khargone, and Ladakh. These three groups had different dietary habits and antibiotic consumption rates. A resistome analysis indicated that compared to the Jaisalmer (n = 10) group, the burden of antibiotic resistance genes in the gut microbiome was higher in the Khargone (n = 12) and Ladakh (n = 9) groups. However, correlational analysis factoring in food habits, healthcare, and economic status was not statistically significant due to the limited number of samples. A considerable number of antibiotic resistance genes (ARGs) were present in well-known gut commensals such as Bifidobacteriaceae, Acidomonococcaceae, etc., as retrieved directly by mapping to the Resfinder database using the Groot tool. Further, the raw reads were assembled using MEGAHIT, and putative bacteriophages were retrieved using the VIBRANT tool. Many of the classified bacteriophages of the virome revealed that bacteria belonging to the families Bifidobacteriaceae and Enterocococcaceae were their hosts. The prophages identified in these groups primarily contained auxiliary metabolic genes (AMGs) for primary amino acid metabolism. However, there were significantly fewer AMGs in the Ladakh group than in the Jaisalmer group (p < 0.05). None of the classified bacteriophages or prophages contained ARGs. This indicates that phages do not normally carry antibiotic resistance genes.},
}
@article {pmid39158621,
year = {2024},
author = {Borah, K and Das, HS and Seth, S and Mallick, K and Rahaman, Z and Mallik, S},
title = {A review on advancements in feature selection and feature extraction for high-dimensional NGS data analysis.},
journal = {Functional &amp; integrative genomics},
volume = {24},
number = {5},
pages = {139},
pmid = {39158621},
issn = {1438-7948},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Machine Learning ; Deep Learning ; },
abstract = {Recent advancements in biomedical technologies and the proliferation of high-dimensional Next Generation Sequencing (NGS) datasets have led to significant growth in the bulk and density of data. The NGS high-dimensional data, characterized by a large number of genomics, transcriptomics, proteomics, and metagenomics features relative to the number of biological samples, presents significant challenges for reducing feature dimensionality. The high dimensionality of NGS data poses significant challenges for data analysis, including increased computational burden, potential overfitting, and difficulty in interpreting results. Feature selection and feature extraction are two pivotal techniques employed to address these challenges by reducing the dimensionality of the data, thereby enhancing model performance, interpretability, and computational efficiency. Feature selection and feature extraction can be categorized into statistical and machine learning methods. The present study conducts a comprehensive and comparative review of various statistical, machine learning, and deep learning-based feature selection and extraction techniques specifically tailored for NGS and microarray data interpretation of humankind. A thorough literature search was performed to gather information on these techniques, focusing on array-based and NGS data analysis. Various techniques, including deep learning architectures, machine learning algorithms, and statistical methods, have been explored for microarray, bulk RNA-Seq, and single-cell, single-cell RNA-Seq (scRNA-Seq) technology-based datasets surveyed here. The study provides an overview of these techniques, highlighting their applications, advantages, and limitations in the context of high-dimensional NGS data. This review provides better insights for readers to apply feature selection and feature extraction techniques to enhance the performance of predictive models, uncover underlying biological patterns, and gain deeper insights into massive and complex NGS and microarray data.},
}
@article {pmid39158294,
year = {2024},
author = {Baker, BJ and Hyde, E and Leão, P},
title = {Nature should be the model for microbial sciences.},
journal = {Journal of bacteriology},
volume = {206},
number = {9},
pages = {e0022824},
pmid = {39158294},
issn = {1098-5530},
support = {LI-SIAME-00002001//Simons Foundation (SF)/ ; },
mesh = {*Bacteria/genetics/classification ; *Archaea/genetics/classification ; },
abstract = {Until recently, microbiologists have relied on cultures to understand the microbial world. As a result, model organisms have been the focus of research into understanding Bacteria and Archaea at a molecular level. Diversity surveys and metagenomic sequencing have revealed that these model species are often present in low abundance in the environment; instead, there are microbial taxa that are cosmopolitan in nature. Due to the numerical dominance of these microorganisms and the size of their habitats, these lineages comprise mind-boggling population sizes upward of 10[28] cells on the planet. Many of these dominant groups have cultured representatives and have been shown to be involved in mediating key processes in nature. Given their importance and the increasing need to understand changes due to climate change, we propose that members of Nitrosophaerota (Nitrosopumilus maritimus), SAR11 (Pelagibacter ubique), Hadesarchaeia, Bathyarchaeia, and others become models in the future. Abundance should not be the only measure of a good model system; there are other organisms that are well suited to advance our understanding of ecology and evolution. For example, the most well-studied symbiotic bacteria, like Buchnera, Aliivibrio, and Rhizobium, should be models for understanding host-associations. Also, there are organisms that hold new insights into major transitions in the evolution of life on the planet like the Asgard Archaea (Heimdallarchaeia). Innovations in a variety of in situ techniques have enabled us to circumvent culturing when studying everything from genetics to physiology. Our deepest understanding of microbiology and its impact on the planet will come from studying these microbes in nature. Laboratory-based studies must be grounded in nature, not the other way around.},
}
@article {pmid39158287,
year = {2024},
author = {Lui, LM and Nielsen, TN},
title = {Decomposing a San Francisco estuary microbiome using long-read metagenomics reveals species- and strain-level dominance from picoeukaryotes to viruses.},
journal = {mSystems},
volume = {9},
number = {9},
pages = {e0024224},
pmid = {39158287},
issn = {2379-5077},
support = {DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; },
mesh = {*Microbiota/genetics ; *Metagenomics/methods ; *Estuaries ; San Francisco ; *Viruses/genetics/classification/isolation &amp; purification ; Metagenome/genetics ; Bacteria/genetics/classification ; Archaea/genetics/virology ; Eukaryota/genetics ; Genome, Viral/genetics ; },
abstract = {UNLABELLED: Although long-read sequencing has enabled obtaining high-quality and complete genomes from metagenomes, many challenges still remain to completely decompose a metagenome into its constituent prokaryotic and viral genomes. This study focuses on decomposing an estuarine metagenome to obtain a more accurate estimate of microbial diversity. To achieve this, we developed a new bead-based DNA extraction method, a novel bin refinement method, and obtained 150 Gbp of Nanopore sequencing. We estimate that there are ~500 bacterial and archaeal species in our sample and obtained 68 high-quality bins (>90% complete, <5% contamination, ≤5 contigs, contig length of >100 kbp, and all ribosomal and tRNA genes). We also obtained many contigs of picoeukaryotes, environmental DNA of larger eukaryotes such as mammals, and complete mitochondrial and chloroplast genomes and detected ~40,000 viral populations. Our analysis indicates that there are only a few strains that comprise most of the species abundances.<br><br>IMPORTANCE: Ocean and estuarine microbiomes play critical roles in global element cycling and ecosystem function. Despite the importance of these microbial communities, many species still have not been cultured in the lab. Environmental sequencing is the primary way the function and population dynamics of these communities can be studied. Long-read sequencing provides an avenue to overcome limitations of short-read technologies to obtain complete microbial genomes but comes with its own technical challenges, such as needed sequencing depth and obtaining high-quality DNA. We present here new sampling and bioinformatics methods to attempt decomposing an estuarine microbiome into its constituent genomes. Our results suggest there are only a few strains that comprise most of the species abundances from viruses to picoeukaryotes, and to fully decompose a metagenome of this diversity requires 1 Tbp of long-read sequencing. We anticipate that as long-read sequencing technologies continue to improve, less sequencing will be needed.},
}
@article {pmid39158216,
year = {2024},
author = {Wang, C and Yang, S and Liu, Q and Liu, H and Jin, S and Zheng, J and Xiao, X and Hou, X and Li, J and Ma, S and Cui, L},
title = {Application of Second-Generation Sequencing Technology in Lower Respiratory Tract Infection.},
journal = {Journal of clinical laboratory analysis},
volume = {},
number = {},
pages = {e25090},
doi = {10.1002/jcla.25090},
pmid = {39158216},
issn = {1098-2825},
support = {//Hospital-Enterprise Joint Funding Project/ ; //Key Clinical Specialty Funding Project of Beijing/ ; },
abstract = {BACKGROUND: Lower respiratory tract infection (LRTI) has long been an important threat to people's life and health, so the rapid diagnosis of LRTI is of great significance in clinical treatment. In recent years, the development of the sequencing technology provides a new direction for the rapid diagnosis of LRTI. In this review, the advantages and disadvantages of second-generation sequencing techniques represented by metagenomics next-generation sequencing (mNGS) and droplet digital polymerase chain reaction (ddPCR) in LRTI were reviewed. Furthermore, it offers insights into the future trajectory of this technology, highlighting its potential to revolutionise the field of respiratory infection diagnostics.<br><br>OBJECTIVE: This review summarises developments in mechanistic research of second-generation sequencing technology their relationship with clinical practice, providing insights for future research.<br><br>METHODS: Authors conducted a search on PubMed and Web of Science using the professional terms 'Lower respiratory tract infection' and 'droplet digital polymerase chain reaction' and 'metagenomics next generation sequencing'. The obtained literature was then roughly categorised based on their research content. Similar studies were grouped into the same sections, and further searches were conducted based on the keywords of each section.<br><br>RESULTS: Different studies discussed the application of second-generation sequencing technology in LRTI from different angles, including the detection of pathogens of LRTI by mNGS and ddPCR, the prediction ability of drug-resistant bacteria, and comparison with traditional methods. We try to analyse the advantages and disadvantages of the second-generation sequencing technology by combing the research results of mNGS and ddPCR. In addition, the development direction of the second-generation sequencing technology is prospected.},
}
@article {pmid39158107,
year = {2024},
author = {Ming, Y and Abdullah Al, M and Zhang, D and Zhu, W and Liu, H and Cai, L and Yu, X and Wu, K and Niu, M and Zeng, Q and He, Z and Yan, Q},
title = {Insights into the evolutionary and ecological adaption strategies of nirS- and nirK-type denitrifying communities.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e17507},
doi = {10.1111/mec.17507},
pmid = {39158107},
issn = {1365-294X},
support = {SML2020SP004//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; SML2023SP237//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; SML2021SP203//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; SML2023SP205//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; 42377111//National Natural Science Foundation of China/ ; //Ocean Negative Carbon Emissions (ONCE) Program/ ; },
abstract = {Denitrification is a crucial process in the global nitrogen cycle, in which two functionally equivalent genes, nirS and nirK, catalyse the critical reaction and are usually used as marker genes. The nirK gene can function independently, whereas nirS requires additional genes to encode nitrite reductase and is more sensitive to environmental factors than nirK. However, the ecological differentiation mechanisms of those denitrifying microbial communities and their adaptation strategies to environmental stresses remain unclear. Here, we conducted metagenomic analysis for sediments and bioreactor samples from Lake Donghu, China. We found that nirS-type denitrifying communities had a significantly lower horizontal gene transfer frequency than that of nirK-type denitrifying communities, and nirS gene phylogeny was more congruent with taxonomy than that of nirK gene. Metabolic reconstruction of metagenome-assembled genomes further revealed that nirS-type denitrifying communities have robust metabolic systems for energy conservation, enabling them to survive under environmental stresses. Nevertheless, nirK-type denitrifying communities seemed to adapt to oxygen-limited environments with the ability to utilize various carbon and nitrogen compounds. Thus, this study provides novel insights into the ecological differentiation mechanism of nirS and nirK-type denitrifying communities, as well as the regulation of the global nitrogen cycle and greenhouse gas emissions.},
}
@article {pmid39158097,
year = {2024},
author = {Coyle, MC and Elya, CN and Bronski, MJ and Eisen, MB},
title = {Entomophthovirus: An insect-derived iflavirus that infects a behavior-manipulating fungal pathogen of dipterans.},
journal = {G3 (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/g3journal/jkae198},
pmid = {39158097},
issn = {2160-1836},
abstract = {We report a virus infecting Entomophthora muscae, a behavior-manipulating fungal pathogen of dipterans. The virus, which we name Berkeley Entomophthovirus, is a positive-strand RNA virus in the iflaviridae family of capsid-forming viruses, which are mostly known to infect insects. The viral RNA is expressed at high levels in fungal cells in vitro and during in vivo infections of Drosophila melanogaster, and virus particles can be seen intracellularly in E. muscae. This virus, of which we find two closely related variants in our culture of E. muscae, is also closely related to three different viruses reported from metagenomic surveys, two of which were isolated from wild dipterans, and a third isolated from wild ticks. By analyzing sequencing data from these earlier reports, we find abundant reads aligning to E. muscae specifically in the samples from which viral reads were sequenced. These data establish a wide and perhaps obligate association with E. muscae in the wild, consistent with our laboratory data that E. muscae is the host for these closely related viruses. Because of this, we propose the name Entomophthovirus for this group of highly related virus variants. As other members of the iflaviridae have been reported to cause behavioral changes in insects, we speculate on the possibility that Entomophthovirus plays a role in the behavioral manipulation of flies infected with E. muscae.},
}
@article {pmid39157704,
year = {2024},
author = {Jevnikar, BE and Khan, ST and Huffman, N and Pasqualini, I and Surace, PA and Deren, ME and Piuzzi, NS},
title = {Advancements in treatment strategies for periprosthetic joint infections: A comprehensive review.},
journal = {Journal of clinical orthopaedics and trauma},
volume = {55},
number = {},
pages = {102496},
pmid = {39157704},
issn = {0976-5662},
abstract = {Periprosthetic joint infection (PJI) presents a critical challenge in orthopedic care, contributing to significant patient morbidity and healthcare costs. This burden is expected to increase secondary to growing demand for total joint arthroplasty (TJA). Despite the profound significance of PJI, there is currently no universally accepted "gold standard" diagnostic criteria using serum biomarker thresholds; latest criteria fail to differentiate acute infections from chronic or consider time since initial surgery. Furthermore, contemporary PJI treatment, which conventionally requires 2-stage revision surgery in conjunction with rigorous antibiotic treatment, can be particularly taxing on patients. Fortunately, recent years have seen marked evolution in both PJI diagnosis and treatment methods. Contemporary research supports time-dependent serum biomarker thresholds with greater sensitivity and specificity than previously reported, as well as alternative surgical options which may be more suitable for certain patients. The following narrative review aims to describe the significance and pathogenesis of PJI before characterizing current challenges, novel innovations, and the future landscape of PJI diagnosis and management. Here, we spotlight the emerging utility of novel biomarkers and metagenomic next-generation sequencing for diagnosis, advancements in patient-centered surgical outcome prediction tools for PJI risk assessment and prevention, and evolving surgical techniques including 1-stage and a "hybrid" 1.5-stage revision surgeries. Additionally, we explore cutting-edge therapeutic modalities including peptide and bacteriophage-based treatments, intraoperative anti-biofilm gel, the VT-X7 antibiotic pump, and promising immune-based interventions. Ultimately, these advancements hold the potential to revolutionize PJI management, offering hope for improved outcomes and reduced burdens on healthcare systems.},
}
@article {pmid39157462,
year = {2024},
author = {Salgado, JFM and Premkrishnan, BNV and Oliveira, EL and Vettath, VK and Goh, FG and Hou, X and Drautz-Moses, DI and Cai, Y and Schuster, SC and Junqueira, ACM},
title = {The dynamics of the midgut microbiome in Aedes aegypti during digestion reveal putative symbionts.},
journal = {PNAS nexus},
volume = {3},
number = {8},
pages = {pgae317},
pmid = {39157462},
issn = {2752-6542},
abstract = {Blood-feeding is crucial for the reproductive cycle of the mosquito Aedes aegypti, as well as for the transmission of arboviruses to hosts. It is postulated that blood meals may influence the mosquito microbiome but shifts in microbial diversity and function during digestion remain elusive. We used whole-genome shotgun metagenomics to monitor the midgut microbiome in 60 individual females of A. aegypti throughout digestion, after 12, 24, and 48 h following blood or sugar meals. Additionally, ten individual larvae were sequenced, showing microbiomes dominated by Microbacterium sp. The high metagenomic coverage allowed for microbial assignments at the species taxonomic level, also providing functional profiling. Females in the post-digestive period and larvae displayed low microbiome diversities. A striking proliferation of Enterobacterales was observed during digestion in blood-fed mosquitoes. The compositional shift was concomitant with enrichment in genes associated with carbohydrate and protein metabolism, as well as virulence factors for antimicrobial resistance and scavenging. The bacterium Elizabethkingia anophelis (Flavobacteriales), a known human pathogen, was the dominant species at the end of blood digestion. Phylogenomics suggests that its association with hematophagous mosquitoes occurred several times. We consider evidence of mutually beneficial host-microbe interactions raised from this association, potentially pivotal for the mosquito's resistance to arbovirus infection. After digestion, the observed shifts in blood-fed females' midguts shifted to a sugar-fed-like microbial profile. This study provides insights into how the microbiome of A. aegypti is modulated to fulfil digestive roles following blood meals, emphasizing proliferation of potential symbionts in response to the dynamic midgut environment.},
}
@article {pmid39157177,
year = {2024},
author = {Huang, SS and Qiu, JY and Li, SP and Ma, YQ and He, J and Han, LN and Jiao, LL and Xu, C and Mao, YM and Zhang, YM},
title = {Microbial signatures predictive of short-term prognosis in severe pneumonia.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1397717},
pmid = {39157177},
issn = {2235-2988},
mesh = {Humans ; Male ; Female ; Prognosis ; Retrospective Studies ; Middle Aged ; Aged ; *Bronchoalveolar Lavage Fluid/microbiology ; *Microbiota ; Pneumonia/microbiology/mortality ; Bacteria/classification/genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; Lung/microbiology/pathology ; Metagenomics ; Machine Learning ; },
abstract = {OBJECTIVE: This retrospective cohort study aimed to investigate the composition and diversity of lung microbiota in patients with severe pneumonia and explore its association with short-term prognosis.<br><br>METHODS: A total of 301 patients diagnosed with severe pneumonia underwent bronchoalveolar lavage fluid metagenomic next-generation sequencing (mNGS) testing from February 2022 to January 2024. After applying exclusion criteria, 236 patients were included in the study. Baseline demographic and clinical characteristics were compared between survival and non-survival groups. Microbial composition and diversity were analyzed using alpha and beta diversity metrics. Additionally, LEfSe analysis and machine learning methods were employed to identify key pathogenic microorganism associated with short-term mortality. Microbial interaction modes were assessed through network co-occurrence analysis.<br><br>RESULTS: The overall 28-day mortality rate was 37.7% in severe pneumonia. Non-survival patients had a higher prevalence of hypertension and exhibited higher APACHE II and SOFA scores, higher procalcitonin (PCT), and shorter hospitalization duration. Microbial &#x3b1; and &#x3b2; diversity analysis showed no significant differences between the two groups. However, distinct species diversity patterns were observed, with the non-survival group showing a higher abundance of Acinetobacter baumannii, Klebsiella pneumoniae, and Enterococcus faecium, while the survival group had a higher prevalence of Corynebacterium striatum and Enterobacter. LEfSe analysis identified 29 distinct terms, with 10 potential markers in the non-survival group, including Pseudomonas sp. and Enterococcus durans. Machine learning models selected 16 key pathogenic bacteria, such as Klebsiella pneumoniae, significantly contributing to predicting short-term mortality. Network co-occurrence analysis revealed greater complexity in the non-survival group compared to the survival group, with differences in central genera.<br><br>CONCLUSION: Our study highlights the potential significance of lung microbiota composition in predicting short-term prognosis in severe pneumonia patients. Differences in microbial diversity and composition, along with distinct microbial interaction modes, may contribute to variations in short-term outcomes. Further research is warranted to elucidate the clinical implications and underlying mechanisms of these findings.},
}
@article {pmid39155949,
year = {2024},
author = {Hu, P and Qian, Y and Xu, Y and Radian, A and Yang, Y and Gu, JD},
title = {A positive contribution to nitrogen removal by a novel NOB in a full-scale duck wastewater treatment system.},
journal = {Water research X},
volume = {24},
number = {},
pages = {100237},
pmid = {39155949},
issn = {2589-9147},
abstract = {Nitrite-oxidizing bacteria (NOB) are undesirable in the anaerobic ammonium oxidation (anammox)-driven nitrogen removal technologies in the modern wastewater treatment plants (WWTPs). Diverse strategies have been developed to suppress NOB based on their physiological properties that we have understood. But our knowledge of the diversity and mechanisms employed by NOB for survival in the modern WWTPs remains limited. Here, Three NOB species (NOB01-03) were recovered from the metagenomic datasets of a full-scale WWTP treating duck breeding wastewater. Among them, NOB01 and NOB02 were classified as newly identified lineage VII, tentatively named Candidatus (Ca.) Nitrospira NOB01 and Ca. Nitrospira NOB02. Analyses of genomes and in situ transcriptomes revealed that these two novel NOB were active and showed a high metabolic versatility. The transcriptional activity of Ca. Nitrospira could be detected in all tanks with quite different dissolved oxygen (DO) (0.01-5.01 mg/L), illustrating Ca. Nitrospira can survive in fluctuating DO conditions. The much lower Ca. Nitrospira abundance on the anammox bacteria-enriched sponge carrier likely originated from the intensification substrate (NO2 [-]) competition from anammox and denitrifying bacteria. In particular, a highlight is that Ca. Nitrospira encoded and treanscribed cyanate hydratase (CynS), amine oxidase, urease (UreC), and copper-containing nitrite reductase (NirK) related to ammonium and NO production, driving NOB to interact with the co-existed AOB and anammox bacteria. Ca. Nitrospira strains NOB01 and NOB02 showed quite different niche preference in the same aerobic tank, which dominanted the NOB communities in activated sludge and biofilm, respectively. In addition to the common rTCA cycle for CO2 fixation, a reductive glycine pathway (RGP) was encoded and transcribed by NOB02 likely for CO2 fixation purpose. Additionally, a 3b group hydrogenase and respiratory nitrate reductase were uniquely encoded and transcribed by NOB02, which likely confer a survival advantage to this strain in the fluctuant activated sludge niche. The discovery of this new genus significantly broadens our understanding of the ecophysiology of NOB. Furthermore, the impressive metabolic versatility of the novel NOB revealed in this study advances our understanding of the survival strategy of NOB and provides valuable insight for suppressing NOB in the anammox-based WWTP.},
}
@article {pmid39155347,
year = {2024},
author = {Dos-Santos, CM and Nascimento, WBA and Cesar, MJSC and Baldani, JI and Schwab, S},
title = {Diversity of bacteria of the genus Sphingomonas associated with sugarcane (Saccharum spp.) culm apoplast fluid and their agrotechnological potential.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {40},
number = {10},
pages = {304},
pmid = {39155347},
issn = {1573-0972},
support = {015/2014//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 12.16.05.017.00.00//Empresa Brasileira de Pesquisa Agropecu&#xe1;ria/ ; },
mesh = {*Saccharum/microbiology ; *Sphingomonas/isolation &amp; purification/classification/genetics ; *Phylogeny ; *RNA, Ribosomal, 16S/genetics ; *In Situ Hybridization, Fluorescence ; DNA, Bacterial/genetics ; Plant Roots/microbiology ; Plant Leaves/microbiology ; Sequence Analysis, DNA ; },
abstract = {In sugarcane, sequences related to the genus Sphingomonas have been widely detected by microbiome studies. In this work, the presence of bacteria of this genus was confirmed using culture-dependent and independent techniques. A collection of thirty isolates was obtained using semispecific cultivation conditions, and a specific PCR assay was applied to help confirm the isolates as belonging to the genus. A series of laboratory evaluations were carried out to identify potential properties among the isolates in the collection, which consequently allowed the identification of some most promising isolates for the development of new agricultural bioinputs. In a separate analysis, the culture-independent fluorescence in situ hybridization (FISH) methodology was applied to demonstrate the natural occurrence of Sphingomonas in different organs and tissues of sugarcane. The results showed the presence of bacteria of the genus in the spaces between cells (apoplast) of the culm parenchyma, in vessels in the region of the leaf vein, on the adaxial surface of the leaf blade, and on the root surface, sometimes close to the base of root hairs, which suggests extensive colonization on the host plant. In summary, the present study corroborates previous metagenomic amplicon sequencing results that indicated a high occurrence of Sphingomonas associated with sugarcane. This is the first study that uses approaches other than amplicon sequencing to confirm the occurrence of the genus in sugarcane and, at the same time, demonstrates potentially beneficial activities to be explored by sugarcane cultivation.},
}
@article {pmid39155203,
year = {2024},
author = {Zhang, P and Lu, Z and Cao, L and Fu, L and Chen, H and Sun, Y},
title = {Diagnostic performance of pancreatic fluid aspiration through metagenomic next-generation sequencing for suspected infected pancreatic necrosis.},
journal = {Digestive and liver disease : official journal of the Italian Society of Gastroenterology and the Italian Association for the Study of the Liver},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.dld.2024.07.036},
pmid = {39155203},
issn = {1878-3562},
abstract = {AIMS: This study aimed to evaluate the diagnostic performance of metagenomic next-generation sequencing (mNGS) with pancreatic fluid aspiration for the detection of infected pancreatic necrosis (IPN).<br><br>METHODS: This retrospective observational study included 66 patients with suspected IPN. The participants simultaneously underwent pancreatic fluid aspiration mNGS, and microbial and blood culture. We compared the diagnostic performance of mNGS with that of culture in the detection of pathogens associated with IPN.<br><br>RESULTS: Of the 66 patients, 45 (68.2 %) were confirmed to have IPN. Pancreatic fluid aspiration mNGS yielded positive results in 32 of these patients (71.1 %), significantly outperforming microbial culture results (25 patients, 55.6 %; P = 0.039); however, both methods exhibited similar specificity (95.2% vs. 100 %). The results of pancreatic fluid aspiration mNGS and microbial culture matched in 73.3 % (33/45) of patients with IPN. The turnaround time for the mNGS results was significantly shorter than that for the microbial culture method (P < 0.001). In addition, survival analysis demonstrated that a positive mNGS result was not associated with increased mortality (hazard ratio, 0.652; 95 % confidence interval 0.157-2.699, P = 0.555).<br><br>CONCLUSIONS: Our study highlights the potential of mNGS for diagnosing IPN, with implications for improving patient care by facilitating early and accurate diagnosis, guiding appropriate interventions, and possibly improving patient outcomes.},
}
@article {pmid39155040,
year = {2024},
author = {Zhang, J and Wang, L and Li, H and Yu, J and Wang, H},
title = {Effect of elemental sulfur on anaerobic ammonia oxidation: Performance and mechanism.},
journal = {Environmental research},
volume = {262},
number = {Pt 1},
pages = {119778},
doi = {10.1016/j.envres.2024.119778},
pmid = {39155040},
issn = {1096-0953},
abstract = {Biological nitrogen removal processes provide effective means to mitigate nitrogen-related issues in wastewater treatment. Previous studies have highlighted the collaborative efficiency between sulfur autotrophic denitrification and Anammox processes. However, the trigger point induced the combination of nitrogen and sulfur metabolism is unclear. In this study, elemental sulfur (S[0]) was introduced to Anammox system to figure out the performance and mechanism of S[0]-mediated autotrophic denitrification and Anammox (S[0]SAD-A) systems. The results showed that the nitrogen removal performance of the Anammox reactor decreased with the increasing concentrations of NH4[+]-N and NO2[-]-N in influent, denitrification occurred when NH4[+]-N concentration reached 100 mg/L. At stage ⅳ (150 mg/L NH4[+]-N), the total nitrogen removal efficiency in S[0]SAD-A system (95.99%) was significantly higher than that in the Anammox system (77.22%). Throughout a hydraulic retention time, the consumption rate of NH4[+]-N in S[0]SAD-A was faster than that in Anammox reactor. And there existed a nitrate-concentration peak in S[0]SAD-A system. Metagenomic sequencing was performed to reveal functional microbes as well as key genes involved in sulfur and nitrogen metabolism. The results showed that the introduction of S[0] elevated the abundance of Ca. Brocadia. Moreover, the relative abundance of Anammox genes, such as hao, hzsA and hzsC were also stimulated by sulfur. Notably, unclassified members in Rhodocyclaceae acted as the primary contributor to key genes involved in the sulfur metabolism. Overall, the interactions between Anammox and denitrification were stimulated by sulfur metabolism. Our study shed light on the potential significance of Rhodocyclaceae members in the S[0]SAD-A process and disclosed the relationship between anammox and denitrification.},
}
@article {pmid39155018,
year = {2024},
author = {Jin, Z and Liang, L and Zhao, Z and Zhang, Y},
title = {Enhancing assimilatory sulfate reduction with ferrihydrite-humic acid coprecipitate in anaerobic sulfate-containing wastewater treatment.},
journal = {Bioresource technology},
volume = {411},
number = {},
pages = {131308},
doi = {10.1016/j.biortech.2024.131308},
pmid = {39155018},
issn = {1873-2976},
mesh = {*Sulfates/metabolism/chemistry ; *Ferric Compounds/chemistry ; *Wastewater/chemistry ; Anaerobiosis ; *Humic Substances ; *Oxidation-Reduction ; *Water Purification/methods ; },
abstract = {Sulfide produced from dissimilatory sulfate reduction can combine with hydrogen to form hydrogen sulfide, causing odor issues and environmental pollution. To address this problem, ferrihydrite-humic acid coprecipitate was added to improve assimilatory sulfate reduction (ASR), resulting in a decrease in sulfide production (190.2 ± 14.6 mg/L in the Fh-HA group vs. 246.3 ± 8.1 mg/L in the Fh group) with high sulfate removal. Humic acid, adsorbed on the surface of ferrihydrite, delayed secondary mineralization of ferrihydrite under sulfate reduction condition. Therefore, more iron-reducing species (e.g. Trichococcus, Geobacter) were enriched with ferrihydrite-humic acid coprecipitate to transfer more electrons to other species, which led to more COD reduction, an increase in electron transfer capacity, and a decrease in the NADH/NAD[+] ratio. Metagenomic analysis also indicated that functional genes related to ASR was enhanced with ferrihydrite-humic acid coprecipitate. Thus, the addition of ferrihydrite-humic acid coprecipitate can be considered as a promising candidate for anaerobic sulfate wastewater treatment.},
}
@article {pmid39154684,
year = {2024},
author = {Li, C and Zhou, X and Wang, J and Ye, H and Sun, C and Alhomrani, M and Alamri, AS and Guo, N},
title = {Preparation of sanguinarine/glabridin loaded antifungal double-layer nanoemulsion edible coating using arabic gum/WPI for forest frog's oviduct oil preservation.},
journal = {International journal of biological macromolecules},
volume = {278},
number = {Pt 2},
pages = {134826},
doi = {10.1016/j.ijbiomac.2024.134826},
pmid = {39154684},
issn = {1879-0003},
mesh = {*Emulsions ; Animals ; *Antifungal Agents/pharmacology/chemistry ; Female ; *Gum Arabic/chemistry ; Benzophenanthridines/chemistry/pharmacology ; Whey Proteins/chemistry/pharmacology ; Microbial Sensitivity Tests ; Isoquinolines ; },
abstract = {Forest frog's oviduct oil (FFOO) is highly susceptible to microbial spoilage during storage, which causes serious safety concerns and economic losses. However, little information is available regarding the preservation of it up to now. The aim of this research is to understand the dominant microbial community of FFOO spoilage, and based on this, develop a kind of edible nanoemulsion coating for preserving FFOO. Microbial metagenomic analysis indicated that the Aspergillus genus increased significantly during storage. In the present study, gum arabic and whey protein isolate were chosen as the coating matrix, the natural compounds sanguinarine and glabridin were selected as antimicrobial agents to prepare double-layer nanoemulsion edible coating. When the ratio of sanguinarine and glabridin in the nanoemulsion was 1:3, it exhibited strongest storage stability and antifungal activity. The mycelial inhibition rate of 1:3 nanoemulsion against dominant microbial community (Aspergillus niger and Aspergillus glaucus) reached 88.89 ± 1.37 % and 89.68 ± 1.37 %, respectively. The experimental results indicated that the edible nanoemulsion coating not only had outstanding antifungal activity, but also had excellent fresh-keeping effect on FFOO. This nanoemulsion coating could be a promising and potential candidate for food preservation.},
}
@article {pmid39154675,
year = {2024},
author = {Ariaeenejad, S and Barani, M and Roostaee, M and Lohrasbi-Nejad, A and Mohammadi-Nejad, G and Hosseini Salekdeh, G},
title = {Enhanced pollutant degradation via green-synthesized core-shell mesoporous Si@Fe magnetic nanoparticles immobilized with metagenomic laccase.},
journal = {International journal of biological macromolecules},
volume = {278},
number = {Pt 2},
pages = {134813},
doi = {10.1016/j.ijbiomac.2024.134813},
pmid = {39154675},
issn = {1879-0003},
mesh = {*Laccase/chemistry/metabolism ; *Enzymes, Immobilized/chemistry/metabolism ; *Magnetite Nanoparticles/chemistry ; *Water Pollutants, Chemical/chemistry ; *Green Chemistry Technology/methods ; Hydrogen-Ion Concentration ; Wastewater/chemistry ; Temperature ; Porosity ; Rosaniline Dyes/chemistry ; Enzyme Stability ; Iron/chemistry ; Water Purification/methods ; Metagenome ; },
abstract = {With rapid industrial expansion, environmental pollution from emerging contaminants has increased, posing severe ecosystem threats. Laccases offer an eco-friendly solution for degrading hazardous substances, but their use as free-form biocatalysts face challenges. This study immobilized laccase (PersiLac1) on green-synthesized Si@Fe nanoparticles (MSFM NPs) to remove pollutants like Malachite Green-containing wastewater and degrade plastic films. Characterization techniques (FTIR, VSM, XRD, SEM, EDS, BET) confirmed the properties and structure of MSFM NPs, revealing a surface area of 31.297 m[2].g[-1] and a pore diameter of 12.267 nm. The immobilized PersiLac1 showed enhanced activity across various temperatures and pH levels, retaining over 82 % activity after 15 cycles at 80°C with minimal leaching. It demonstrated higher stability, half-life, and decimal reduction time than free laccase. Under 1 M NaCl, its activity was 1.8 times higher than the non-immobilized enzyme. The immobilized laccase removed 98.11 % of Malachite Green-containing wastewater and retained 82.92 % activity over twenty cycles of dye removal. Additionally, FTIR and SEM confirmed superior plastic degradation under saline conditions. These findings suggest that immobilizing PersiLac1 on magnetic nanoparticles enhances its function and potential for contaminant removal. Future research should focus on scalable, cost-effective laccase immobilization methods for large-scale environmental applications.},
}
@article {pmid39154625,
year = {2024},
author = {Juli, MSB and Boe-Hansen, GB and Raza, A and Forutan, M and Ong, CT and Siddle, HV and Tabor, AE},
title = {A systematic review of predictive, diagnostic, and prognostic biomarkers for detecting reproductive diseases in cattle using traditional and omics approaches.},
journal = {Journal of reproductive immunology},
volume = {165},
number = {},
pages = {104315},
doi = {10.1016/j.jri.2024.104315},
pmid = {39154625},
issn = {1872-7603},
mesh = {Animals ; Cattle ; *Biomarkers/metabolism ; Female ; *Cattle Diseases/diagnosis/immunology ; Male ; Reproduction/immunology ; Prognosis ; Cytokines/metabolism ; Proteomics/methods ; Metabolomics/methods ; },
abstract = {Reproductive diseases and illnesses pose significant challenges in cattle farming, affecting fertility, milk production, and overall herd health. In recent years, the integration of various omics approaches, including transcriptomics, proteomics, metagenomics, miRNAomics, and metabolomics, has revolutionized the study of these conditions. This systematic review summarised the findings from studies that investigated reproductive disease biomarkers in both male and female cattle. After extracting 6137 studies according to exclusion and inclusion criteria, a total of 60 studies were included in this review. All studies identified were associated with female cattle and none were related to reproductive diseases in bulls. The analysis highlights specific biomarkers, metabolic pathways, and microbial compositions associated with bovine reproductive disease conditions, providing valuable insights into the underlying molecular mechanisms of disease. Pro-inflammatory cytokines such as IL-1β, IL-8, IL-4, IL-6, TNFα and acute-phase response proteins such as SAA and HP have been identified as promising biomarkers for bovine reproductive diseases. However, further research is needed to validate these markers clinically and to explore potential strategies for improving cow reproductive health. The role of bulls as carriers of venereal diseases has been underestimated in the current literature and therefore needs more attention to understand their impact on infectious reproductive diseases of female cattle.},
}
@article {pmid39154602,
year = {2024},
author = {García-Roldán, A and de la Haba, RR and Sánchez-Porro, C and Ventosa, A},
title = {'Altruistic' cooperation among the prokaryotic community of Atlantic salterns assessed by metagenomics.},
journal = {Microbiological research},
volume = {288},
number = {},
pages = {127869},
doi = {10.1016/j.micres.2024.127869},
pmid = {39154602},
issn = {1618-0623},
mesh = {*Metagenomics ; *Bacteria/genetics/classification ; *Salinity ; *Archaea/genetics/classification ; Spain ; Seawater/microbiology ; Phylogeny ; Atlantic Ocean ; Biodiversity ; Salts ; Microbiota/genetics ; Ecosystem ; Metagenome ; },
abstract = {Hypersaline environments are extreme habitats with a limited prokaryotic diversity, mainly restricted to halophilic or halotolerant archaeal and bacterial taxa adapted to highly saline conditions. This study attempts to analyze the taxonomic and functional diversity of the prokaryotes that inhabit a solar saltern located at the Atlantic Coast, in Isla Cristina (Huelva, Southwest Spain), and the influence of salinity on the diversity and metabolic potential of these prokaryotic communities, as well as the interactions and cooperation among the individuals within that community. Brine samples were obtained from different saltern ponds, with a salinity range between 19.5 % and 39 % (w/v). Total prokaryotic DNA was sequenced using the Illumina shotgun metagenomic strategy and the raw sequence data were analyzed using supercomputing services following the MetaWRAP and SqueezeMeta protocols. The most abundant phyla at moderate salinities (19.5-22 % [w/v]) were Methanobacteriota (formerly "Euryarchaeota"), Pseudomonadota and Bacteroidota, followed by Balneolota and Actinomycetota and Uroviricota in smaller proportions, while at high salinities (36-39 % [w/v]) the most abundant phylum was Methanobacteriota, followed by Bacteroidota. The most abundant genera at intermediate salinities were Halorubrum and the bacterial genus Spiribacter, while the haloarchaeal genera Halorubrum, Halonotius, and Haloquadratum were the main representatives at high salinities. A total of 65 MAGs were reconstructed from the metagenomic datasets and different functions and pathways were identified in them, allowing to find key taxa in the prokaryotic community able to synthesize and supply essential compounds, such as biotin, and precursors of other bioactive molecules, like β-carotene, and bacterioruberin, to other dwellers in this habitat, lacking the required enzymatic machinery to produce them. This work shed light on the ecology of aquatic hypersaline environments, such as the Atlantic Coast salterns, and on the dynamics and factors affecting the microbial populations under such extreme conditions.},
}
@article {pmid39154578,
year = {2024},
author = {Liang, T and Liu, Y and Guo, N and Li, Y and Niu, L and Liu, J and Ma, Q and Zhang, J and Shan, M},
title = {Jinhong decoction ameliorates injury in septic mice without disrupting the equilibrium of gut microbiota.},
journal = {Journal of pharmaceutical and biomedical analysis},
volume = {251},
number = {},
pages = {116404},
doi = {10.1016/j.jpba.2024.116404},
pmid = {39154578},
issn = {1873-264X},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Sepsis/drug therapy/microbiology ; *Drugs, Chinese Herbal/pharmacology ; Mice ; Male ; *Disease Models, Animal ; Anti-Bacterial Agents/pharmacology ; Chromatography, High Pressure Liquid/methods ; Cecum/microbiology ; Mice, Inbred C57BL ; },
abstract = {Sepsis is a life-threatening condition and usually be treated with antibiotics, which however often has severe side effects. This work proposed a novel Chinese traditional medicine JINHONG (JH) decoction for therapy of sepsis. We first identified the chemical constituents of JH decoction by using high-performance liquid chromatography and mass spectrometry (HPLC-MS). Then, we constructed a model mouse for sepsis by using cecal ligation and puncture (CLP). Metagenomic sequencing method was used to compare the diversity and abundance of the gut microbiota between normal, disease model, JH decoction-treatment and antibiotic-treatment mice. Many indices including the number of platelets, CD62p and CD63 content, AQP2 and AQP8 level, as well as the expression level of protein C confirmed that the sepsis resulted in serious pathological damage, while all of these indices could be reversed by JH decoction and antibiotics. The diversity and abundance of intestinal flora decreased in CLP mice, and the decrements aggravated after antibiotic treatment while can be recovered by JH decoction treatment. The abundance of anti-inflammatory Ruminococcaceae increased after JH decoction treatment, indicating that JH decoction could ameliorate pathology associated with sepsis in CLP model via modulating the intestinal flora. This study demonstrates that JH decoction could treat sepsis clinically without obvious adverse effects on gut microbiota.},
}
@article {pmid39154395,
year = {2024},
author = {Deng, D and Yang, Z and Yang, Y and Wan, W and Liu, W and Xiong, X},
title = {Metagenomic insights into nitrogen-cycling microbial communities and their relationships with nitrogen removal potential in the Yangtze River.},
journal = {Water research},
volume = {265},
number = {},
pages = {122229},
doi = {10.1016/j.watres.2024.122229},
pmid = {39154395},
issn = {1879-2448},
mesh = {*Rivers/microbiology ; *Nitrogen/metabolism ; Metagenomics ; Nitrogen Cycle ; China ; Denitrification ; Metagenome ; Bacteria/metabolism/genetics ; },
abstract = {Nitrogen (N) pollution is a major threat to river ecosystems worldwide. Elucidating the community structure of N-cycling microorganisms in rivers is essential to understanding how ecosystem processes and functions will respond to increasing N inputs. However, previous studies generally focus on limited functional genes through amplicon sequencing or quantitative PCR techniques and cannot cover all N-cycling microorganisms. Here, metagenomic sequencing and genome binning were used to determine N-cycling genes in water, channel sediments, and riparian soils of the Yangtze River, which has been heavily polluted by N. Additionally, the denitrification and anaerobic ammonium oxidation (anammox) rates that reflect N removal potential were measured using [15]N isotope pairing technique. Results showed that functional genes involved in organic N metabolism (i.e., organic degradation and synthesis) and nitrate reduction pathways (i.e., dissimilatory and assimilatory nitrate reduction to ammonium and denitrification) were more abundant and diverse than other N-cycling genes. A total of 121 metagenome-assembled genomes (MAGs) were identified to be involved in N-cycling processes, and the key MAGs were mainly taxonomically classified as Alphaproteobacteria and Gammaproteobacteria. The abundance and diversity of most N-cycling genes were higher in soils and sediments than in water, as well as higher in downstream and midstream than in upstream sites. These spatial variations were explained not only by local environment and vegetation but also by geographical and climatic factors. N removal process (i.e., denitrification and anammox) rates were significantly related to the abundance or diversity of several N-cycling genes, and climate and edaphic factors could regulate denitrification and anammox rates directly and indirectly through their effects on functional genes. Overall, these results provide a new avenue for further understanding the biogeographic patterns and environmental drivers of N-cycling microorganisms in rivers from the metagenomic perspective.},
}
@article {pmid39154041,
year = {2024},
author = {Ma, T and Zhuang, Y and Lu, W and Tu, Y and Diao, Q and Fan, X and Zhang, N},
title = {Seven hundred and ninety-seven metagenome-assembled genomes from the goat rumen during early life.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {897},
pmid = {39154041},
issn = {2052-4463},
mesh = {Animals ; *Goats/microbiology ; *Rumen/microbiology ; *Metagenome ; Gastrointestinal Microbiome ; },
abstract = {The rumen microbiome plays an important role in providing energy and protein to the host. Manipulation of rumen microbiome during early life may have a long-term beneficial effect on the health, growth performance, and feed efficiency of ruminants. To better understand the profiles and functional potentials of rumen microbiome in young ruminants, metagenomic binning was performed to investigate the rumen microbiome of goat kids from one to 84 days of age. A total of 797 metagenome-assembled genomes (MAGs) were recovered from the rumen of 42 Laiwu black goat kids. Our findings provide fundamental knowledge of the rumen microbiome during early life based on metagenomic binning, which may provide insights into effective strategies to achieve long-term beneficial effects on animal health and production.},
}
@article {pmid39153763,
year = {2024},
author = {Cleminson, JS and Thomas, J and Stewart, CJ and Campbell, D and Gennery, A and Embleton, ND and Köglmeier, J and Wong, T and Spruce, M and Berrington, JE},
title = {Gut microbiota and intestinal rehabilitation: a prospective childhood cohort longitudinal study of short bowel syndrome (the MIRACLS study): study protocol.},
journal = {BMJ open gastroenterology},
volume = {11},
number = {1},
pages = {},
pmid = {39153763},
issn = {2054-4774},
mesh = {Humans ; *Short Bowel Syndrome/microbiology/epidemiology ; *Gastrointestinal Microbiome/physiology ; *Quality of Life/psychology ; Prospective Studies ; Child ; Child, Preschool ; Infant ; Longitudinal Studies ; Female ; Adolescent ; *Feces/microbiology ; Male ; *Parenteral Nutrition/methods/statistics &amp; numerical data ; Infant, Newborn ; RNA, Ribosomal, 16S ; Intestines/microbiology ; },
abstract = {INTRODUCTION: Short bowel syndrome (SBS) is the predominant cause of paediatric intestinal failure. Although life-saving, parenteral nutrition (PN) is linked to complications and may impact quality of life (QoL). Most children will experience intestinal rehabilitation (IR), but the mechanisms underpinning this remain to be understood. SBS is characterised by abnormal microbiome patterns, which might serve as predictive indicators for IR. We aim to characterise the microbiome profiles of children with SBS during IR, concurrently exploring how parental perspectives of QoL relate to IR.<br><br>METHODS AND ANALYSIS: This study will enrol a minimum of 20 paediatric patients with SBS (0-18 years). Clinical data and biological samples will be collected over a 2-year study period. We will apply 16S rRNA gene sequencing to analyse the microbiome from faecal and gut tissue samples, with additional shotgun metagenomic sequencing specifically on samples obtained around the time of IR. Gas chromatography with flame ionisation detection will profile faecal short-chain fatty acids. Plasma citrulline and urinary intestinal fatty acid binding proteins will be measured annually. We will explore microbiome-clinical covariate interactions. Furthermore, we plan to assess parental perspectives on QoL during PN and post-IR by inviting parents to complete the Paediatric Quality of Life questionnaire at recruitment and after the completion of IR.<br><br>ETHICS AND DISSEMINATION: Ethical approval was obtained from the East Midlands-Nottingham 2 Research Ethics Committee (22/EM/0233; 28 November 2022). Recruitment began in February 2023. Outcomes of the study will be published in peer-reviewed scientific journals and presented at scientific meetings. A lay summary of the results will be made available to participants and the public.<br><br>TRIAL REGISTRATION NUMBER: ISRCTN90620576.},
}
@article {pmid39153640,
year = {2024},
author = {Du, L and Zhong, H and Guo, X and Li, H and Xia, J and Chen, Q},
title = {Nitrogen fertilization and soil nitrogen cycling: Unraveling the links among multiple environmental factors, functional genes, and transformation rates.},
journal = {The Science of the total environment},
volume = {951},
number = {},
pages = {175561},
doi = {10.1016/j.scitotenv.2024.175561},
pmid = {39153640},
issn = {1879-1026},
mesh = {*Fertilizers ; *Nitrogen Cycle ; *Nitrogen/metabolism ; *Soil Microbiology ; *Soil/chemistry ; *Agriculture/methods ; Fungi ; Bacteria ; Phosphorus/analysis ; Ecosystem ; },
abstract = {Anthropogenic nitrogen (N) inputs substantially influence the N cycle in agricultural ecosystems. However, the potential links among various environmental factors, nitrogen functional genes, and transformation rates under N fertilization remain poorly understood. Here, we conducted a five-year field experiment and collected 54 soil samples from three 0-4 m boreholes across different treatments: control, N-addition (nitrogen fertilizer) and NPK-addition (combined application of nitrogen, phosphorus and potassium fertilizers) treatments. Our results revealed pronounced variations in soil physiochemical parameters, metal concentrations and antibiotic levels under both N and NPK treatments. These alternations induced significant shifts in bacterial and fungal communities, altered NFG abundance and composition, and greatly enhanced rates of nitrate reduction processes. Notably, nutrients, antibiotics and bacteria exerted a more pronounced influence on NFGs and nitrate reduction under N treatment, whereas nutrients, metals, bacteria and fungi had a significant impact under NPK treatment. Furthermore, we established multidimensional correlations between nitrate reduction gene profiles and the activity rates under N and NPK treatments, contrasting with the absence of significant relationships in the control treatment. These findings shed light on the intricate relationships between microbial genetics and ecosystem functions in agricultural ecosystem, which is of significance for predicting and managing metabolic processes effectively.},
}
@article {pmid39153624,
year = {2024},
author = {Barquero, MB and García-Díaz, C and Dobbler, PT and Jehmlich, N and Moreno, JL and López-Mondéjar, R and Bastida, F},
title = {Contrasting fertilization and phenological stages shape microbial-mediated phosphorus cycling in a maize agroecosystem.},
journal = {The Science of the total environment},
volume = {951},
number = {},
pages = {175571},
doi = {10.1016/j.scitotenv.2024.175571},
pmid = {39153624},
issn = {1879-1026},
mesh = {*Zea mays ; *Phosphorus/metabolism ; *Fertilizers ; *Soil Microbiology ; Microbiota ; Bacteria/metabolism ; Agriculture/methods ; Archaea/physiology/metabolism ; Soil/chemistry ; },
abstract = {Phosphorus (P) is essential for plants but often limited in soils, with microbes playing a key role in its cycling. P deficiency in crops can be mitigated by applying by-products like sludge and struvite to enhance yield and sustainability. Here, we evaluated the contribution of four different types of fertilizers: i) conventional NPK; ii) sludge; iii) struvite; and iv) struvite+sludge in a semiarid maize plantation to the availability of P and the responses of the soil microbiome. We investigated the effects of these treatments on the relative abundance of bacterial and archaeal genes and proteins related to organic P mineralization, inorganic P solubilization, and the P starvation response regulation through a multi-omic approach. Moreover, we explored the impact of maize phenology by collecting samples at germination and flowering stages. Our findings suggest that the phenological stage has a notable impact on the abundance of P cycle genes within bacterial and archaeal communities, particularly regarding the solubilization of inorganic P. Furthermore, significant variations were observed in the relative abundance of genes associated with different P cycles in response to various fertilizer treatments. Sludge and struvite application improved P availability, which was related to an increase in the relative abundance of Sphingomonas (Proteobacteria) and Luteitalea (Acidobacteria) respectively, and genes related to inorganic P solubilization. Furthermore, we observed a substantial taxonomic clustering of functional processes associated with the P cycle. Among the dominant bacterial populations containing P-related genes, those microbes possessing genes linked to the solubilization of inorganic P typically did not harbor genes associated with the mineralization of organic P. This phenomenon was particularly evident among members of Actinobacteria. Overall, we reveal important shifts in bacterial and archaeal communities and associated molecular processes, stressing the intricate interplay between fertilization, phenology, and P cycling in agroecosystems.},
}
@article {pmid39153612,
year = {2024},
author = {Chen, T and Wang, Z and Ruan, X},
title = {Antibiotic resistome dynamics in agricultural river systems: Elucidating transmission mechanisms and associated risk to water security.},
journal = {The Science of the total environment},
volume = {951},
number = {},
pages = {175580},
doi = {10.1016/j.scitotenv.2024.175580},
pmid = {39153612},
issn = {1879-1026},
mesh = {*Rivers/microbiology ; China ; *Agriculture ; *Drug Resistance, Microbial/genetics ; *Environmental Monitoring ; Anti-Bacterial Agents ; Water Pollutants, Chemical/analysis ; },
abstract = {Usage of antibiotics in agriculture has increased dramatically recently, significantly raising the influx of antibiotic resistance genes (ARGs) into river systems through organic manure runoff, seriously threatening water security. However, the dynamics, transmission mechanisms, and potential water security risk of ARGs, as well as their response to land use spatial scale and seasonal variations in agricultural river systems remain unclear. To address these challenges, this work employed metagenomic technique to systematically evaluate the pollution and dissemination of ARGs in overlying water and sediment within a typical agricultural catchment in China. The results demonstrated significant differences between overlying water and sediment ARGs. Overlying water dominated by multidrug ARGs exhibited higher diversity, whereas sediment predominantly containing sulfonamide ARGs had higher abundance. The dynamics of ARGs in overlying water were more responsive to seasonal variations compared to sediment due to greater changes in hydrodynamics and nutrient conditions. The profiles of ARGs in overlying water were largely regulated by microbiota, whereas mobile genetic elements (MGEs) were the main forces driving the dissemination of ARGs in sediment. The variation in dissemination mechanisms led to different resistance risks, with sediment presenting a higher resistance risk than overlying water. Furthermore, Mantel test was applied to discover the impact of land use spatial scale and composition on the transmission of ARGs in river systems. The findings showed that cultivated land within 5 km of the riverbank was the key influencing factor. Cultivated land exacerbated ARGs spread by increasing MGEs abundance and nutrient concentrations, resulting in the abundance of ARGs in high-cultivated sites being twice that in low-cultivated sites, and raising the regional water security risk, with a more pronounced effect in sediment. These findings contribute to a better understanding of ARGs dissemination in agricultural watersheds, providing a basis for implementing effective resistance control measures and ensuring water security.},
}
@article {pmid39153565,
year = {2024},
author = {Yang, C and Yan, S and Zhang, B and Yao, X and Mo, J and Rehman, F and Guo, J},
title = {Spatiotemporal distribution of the planktonic microbiome and antibiotic resistance genes in a typical urban river contaminated by macrolide antibiotics.},
journal = {Environmental research},
volume = {262},
number = {Pt 1},
pages = {119808},
doi = {10.1016/j.envres.2024.119808},
pmid = {39153565},
issn = {1096-0953},
abstract = {The widespread application of macrolide antibiotics has caused antibiotic resistance pollution, threatening the river ecological health. In this study, five macrolide antibiotics (azithromycin, clarithromycin, roxithromycin, erythromycin, and anhydro erythromycin A) were monitored in the Zao River across three hydrological periods (April, July, and December). Simultaneously, the changes in antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and planktonic bacterial communities were determined using metagenomic sequencing. A clear pollution gradient was observed for azithromycin and roxithromycin, with the concentrations in the dry season surpassing those in other seasons. The highest concentration was observed for azithromycin (1.36 μg/L). The abundance of MLS resistance genes increased along the Zao River during the dry season, whereas the opposite trend was obtained during the wet season. A significant correlation between the levels of MLS resistance genes and macrolide antibiotics was identified during the dry season. Notably, compared with the reference site, the abundance of transposase in the effluent from wastewater treatment plants (WWTPs) was significantly elevated in both dry and wet seasons, whereas the abundance of insertion sequences (IS) and plasmids declined during the dry season. The exposure to wastewater containing macrolide antibiotics altered the diversity of planktonic bacterial communities. The bacterial host for ARGs appeared to be Pseudomonas, primarily associated with multidrug subtypes. Moreover, the ARG subtypes were highly correlated with MGEs (transposase and istA). The partial least-squares path model (PLS-PM) demonstrated a positive correlation between the abundance of MGEs and ARGs, indicating the significance of horizontal gene transfer (HGT) in the dissemination of ARGs within the Zao River. Environmental variables, such as TN and NO3[-]-N, were significantly correlated with the abundance of MGEs, ARGs, and bacteria. Collectively, our findings could provide insights into the shift patterns of the microbiome and ARGs across the contamination gradient of AZI and ROX in the river.},
}
@article {pmid39153385,
year = {2024},
author = {Shen, J and Yu, D and Liu, Z and Di, H and He, JZ},
title = {Land use conversion to uplands significantly increased the risk of antibiotic resistance genes in estuary area.},
journal = {Environment international},
volume = {191},
number = {},
pages = {108953},
doi = {10.1016/j.envint.2024.108953},
pmid = {39153385},
issn = {1873-6750},
mesh = {*Estuaries ; *Wetlands ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Metagenomics ; Agriculture ; Anti-Bacterial Agents ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Land use conversion in estuary wetlands may affect the transmission of antibiotic resistance genes (ARGs), while the risk rank of the ARGs and the change of clinically relevant ARGs under various land-use types are not well understood. This study used metagenomics to reveal the diversity and abundance of ARGs across five distinct land uses: reed wetland, tidal flat, grassland, agricultural land and fallow land, as well as their distribution and potential health risks. Results showed that high numbers of ARG subtypes and classes were detected irrespective of land-use types, notably higher in agricultural land (144 ARG subtypes). The most shared ARG subtypes were multidrug resistance genes across all the land uses (29 subtypes, 4.7 × 10[-2]-1.5 × 10[-1] copies per 16S rRNA gene copy). Proteobacteria and Actinobacteria were primary ARG hosts, with 18 and 15 ARGs were found in both of them, respectively. The ARG subtype mdtB was the most dominant clinical ARG detected with 90 % amino acid identity. The change of ARGs exhibited a consistent trend across land uses in terms of health risk ranks, with the highest observed in fallow land and the lowest in reed wetland. This study reveals the distribution pattern of ARGs across various land-use types, and enhances our understanding of the potential health risks associated with ARGs in the context of coastal wetland conversion in estuary areas.},
}
@article {pmid39152482,
year = {2024},
author = {Luo, W and Zhao, M and Dwidar, M and Gao, Y and Xiang, L and Wu, X and Medema, MH and Xu, S and Li, X and Schäfer, H and Chen, M and Feng, R and Zhu, Y},
title = {Microbial assimilatory sulfate reduction-mediated H2S: an overlooked role in Crohn's disease development.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {152},
pmid = {39152482},
issn = {2049-2618},
support = {82370551//National Natural Science Foundation of China/ ; 82270579//National Natural Science Foundation of China/ ; 82100577//National Natural Science Foundation of China/ ; 2024GXNSFFA010009//Natural Science Foundation of Guangxi Zhuang Autonomous Region/ ; },
mesh = {*Crohn Disease/microbiology ; Humans ; *Gastrointestinal Microbiome ; *Hydrogen Sulfide/metabolism ; Animals ; Mice ; *Sulfates/metabolism ; Escherichia coli/genetics/metabolism ; Feces/microbiology ; Dysbiosis/microbiology ; Colon/microbiology ; Metagenomics ; Oxidation-Reduction ; Disease Models, Animal ; Female ; },
abstract = {BACKGROUND: H2S imbalances in the intestinal tract trigger Crohn's disease (CD), a chronic inflammatory gastrointestinal disorder characterized by microbiota dysbiosis and barrier dysfunction. However, a comprehensive understanding of H2S generation in the gut, and the contributions of both microbiota and host to systemic H2S levels in CD, remain to be elucidated. This investigation aimed to enhance comprehension regarding the sulfidogenic potential of both the human host and the gut microbiota.<br><br>RESULTS: Our analysis of a treatment-naive CD cohorts' fecal metagenomic and biopsy metatranscriptomic data revealed reduced expression of host endogenous H2S generation genes alongside increased abundance of microbial exogenous H2S production genes in correlation with CD. While prior studies focused on microbial H2S production via dissimilatory sulfite reductases, our metagenomic analysis suggests the assimilatory sulfate reduction (ASR) pathway is a more significant contributor in the human gut, given its high prevalence and abundance. Subsequently, we validated our hypothesis experimentally by generating ASR-deficient E. coli mutants &#x2206;cysJ and &#x2206;cysM through the deletion of sulfite reductase and L-cysteine synthase genes. This alteration significantly affected bacterial sulfidogenic capacity, colon epithelial cell viability, and colonic mucin sulfation, ultimately leading to colitis in murine model. Further study revealed that gut microbiota degrade sulfopolysaccharides and assimilate sulfate to produce H2S via the ASR pathway, highlighting the role of sulfopolysaccharides in colitis and cautioning against their use as food additives.<br><br>CONCLUSIONS: Our study significantly advances understanding of microbial sulfur metabolism in the human gut, elucidating the complex interplay between diet, gut microbiota, and host sulfur metabolism. We highlight the microbial ASR pathway as an overlooked endogenous H2S producer and a potential therapeutic target for managing CD. Video Abstract.},
}
@article {pmid39152290,
year = {2024},
author = {Chen, J and Qin, Z and Jia, Z},
title = {The application status of sequencing technology in global respiratory infectious disease diagnosis.},
journal = {Infection},
volume = {},
number = {},
pages = {},
pmid = {39152290},
issn = {1439-0973},
support = {INV-045088//Bill and Melinda Gates Foundation/ ; },
abstract = {Next-generation sequencing (NGS) has revolutionized clinical microbiology, particularly in diagnosing respiratory infectious diseases and conducting epidemiological investigations. This narrative review summarizes conventional methods for routine respiratory infection diagnosis, including culture, smear microscopy, immunological assays, image techniques as well as polymerase chain reaction(PCR). In contrast to conventional methods, there is a new detection technology, sequencing technology, and here we mainly focus on the next-generation sequencing NGS, especially metagenomic NGS(mNGS). NGS offers significant advantages over traditional methods. Firstly, mNGS eliminates assumptions about pathogens, leading to faster and more accurate results, thus reducing diagnostic time. Secondly, it allows unbiased identification of known and novel pathogens, offering broad-spectrum coverage. Thirdly, mNGS not only identifies pathogens but also characterizes microbiomes, analyzes human host responses, and detects resistance genes and virulence factors. It can complement targeted sequencing for bacterial and fungal classification. Unlike traditional methods affected by antibiotics, mNGS is less influenced due to the extended survival of pathogen DNA in plasma, broadening its applicability. However, barriers to full integration into clinical practice persist, primarily due to cost constraints and limitations in sensitivity and turnaround time. Despite these challenges, ongoing advancements aim to improve cost-effectiveness and efficiency, making NGS a cornerstone technology for global respiratory infection diagnosis.},
}
@article {pmid39152146,
year = {2024},
author = {Mizsei, E and Radovics, D and Rák, G and Budai, M and Bancsik, B and Szabolcs, M and Sos, T and Lengyel, S},
title = {Alpine viper in changing climate: thermal ecology and prospects of a cold-adapted reptile in the warming Mediterranean.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {18988},
pmid = {39152146},
issn = {2045-2322},
support = {150510498//Mohamed bin Zayed Species Conservation Fund/ ; 15478-1//Rufford Foundation/ ; PD146621//Nemzeti Kutat&#xe1;si Fejleszt&#xe9;si &#xe9;s Innov&#xe1;ci&#xf3;s Hivatal/ ; K106133//Nemzeti Kutat&#xe1;si Fejleszt&#xe9;si &#xe9;s Innov&#xe1;ci&#xf3;s Hivatal/ ; K134391//Nemzeti Kutat&#xe1;si Fejleszt&#xe9;si &#xe9;s Innov&#xe1;ci&#xf3;s Hivatal,Hungary/ ; },
mesh = {Animals ; *Viperidae/physiology ; *Climate Change ; Male ; Female ; Ecosystem ; Body Temperature Regulation/physiology ; Greece ; Cold Temperature ; Adaptation, Physiological ; Mediterranean Region ; Acclimatization/physiology ; Phylogeny ; Body Temperature/physiology ; },
abstract = {In a rapidly changing thermal environment, reptiles are primarily dependent on in situ adaptation because of their limited ability to disperse and the restricted opportunity to shift their ranges. However, the rapid pace of climate change may surpass these adaptation capabilities or elevate energy expenditures. Therefore, understanding the variability in thermal traits at both individual and population scales is crucial, offering insights into reptiles' vulnerability to climate change. We studied the thermal ecology of the endangered Greek meadow viper (Vipera graeca), an endemic venomous snake of fragmented alpine-subalpine meadows above 1600 m of the Pindos mountain range in Greece and Albania, to assess its susceptibility to anticipated changes in the alpine thermal environment. We measured preferred body temperature in artificial thermal gradient, field body temperatures of 74 individuals in five populations encompassing the entire geographic range of the species, and collected data on the available of temperatures for thermoregulation. We found that the preferred body temperature (Tp) differed only between the northernmost and the southernmost populations and increased with female body size but did not depend on sex or the gravidity status of females. Tp increased with latitude but was unaffected by the phylogenetic position of the populations. We also found high accuracy of thermoregulation in V. graeca populations and variation in the thermal quality of habitats throughout the range. The overall effectiveness of thermoregulation was high, indicating that V. graeca successfully achieves its target temperatures and exploits the thermal landscape. Current climatic conditions limit the activity period by an estimated 1278 h per year, which is expected to increase considerably under future climate scenarios. Restricted time available for thermoregulation, foraging and reproduction will represent a serious threat to the fitness of individuals and the persistence of populations in addition to habitat loss due to mining, tourism or skiing and habitat degradation due to overgrazing in the shrinking mountaintop habitats of V. graeca.},
}
@article {pmid39151634,
year = {2024},
author = {Xu, WJ and Meng, L and Zhao, YK and Wu, J and Liu, HM and Wang, JQ and Zheng, N},
title = {Characteristics of psychrophilic bacterial communities and associated metabolism pathways in different environments by a metagenomic analysis.},
journal = {The Science of the total environment},
volume = {953},
number = {},
pages = {175496},
doi = {10.1016/j.scitotenv.2024.175496},
pmid = {39151634},
issn = {1879-1026},
abstract = {Psychrophilic bacteria, the dominant spoilage organisms in raw milk, secrete heat-stable extracellular proteases and lipases that lead to the decomposition of milk and dairy products. In this study, we investigated psychrophilic bacteria in 165 raw milk samples collected across four seasons and six regions in China using shotgun metagenomic sequencing and traditional culture methods. The isolated psychrophilic bacteria were classified into 40 genera and 185 species. Pseudomonas was the most prevalent, accounting for 51.13 % of the genera, while Lactococcus and Chryseobacterium were also notably abundant (> 6.0 %). Metagenomic sequencing revealed that Pseudomonas (47.9 %), Stenotrophomonas (9.75 %), Sphingomonas (6.73 %), Latilactobacillus (6.38 %) and Lactococcus (5.16 %) were the dominant genera in the raw milk samples. The diversity of psychrophilic bacteria in raw milk was strongly influenced by seasonal variations, with the sampling region being a less significant factor. KEGG annotation indicated that carbohydrate and amino acid metabolism were the primary metabolic pathways in these bacteria. Metagenomic sequencing not only accurately identifies species but also provides functional insights into psychrophilic bacteria in raw milk, aiding in understanding their activities, promoting their control on farms, and ultimately improving raw milk quality.},
}
@article {pmid39151620,
year = {2024},
author = {Zheng, Y and Wu, Z and Wang, P and Wei, Y and Jia, K and Zhang, M and Shi, X and Zhang, L and Li, J},
title = {Long-chain fatty acids facilitate acidogenic fermentation of food waste: Attention to the microbial response and the change of core metabolic pathway under saturated and unsaturated fatty acids loading.},
journal = {The Science of the total environment},
volume = {951},
number = {},
pages = {175565},
doi = {10.1016/j.scitotenv.2024.175565},
pmid = {39151620},
issn = {1879-1026},
mesh = {*Fermentation ; *Fatty Acids/metabolism ; Metabolic Networks and Pathways ; Fatty Acids, Volatile/metabolism ; Fatty Acids, Unsaturated/metabolism ; Food Loss and Waste ; },
abstract = {Long-chain fatty acids (LCFAs) are recognized as a significant inhibitory factor in anaerobic digestion of food waste (FW), yet they are inevitably present in FW due to lipid hydrolysis. Given their distinct synthesis mechanism from traditional anaerobic digestion, little is known about the effect of LCFAs on FW acidogenic fermentation. This study reveals that total volatile fatty acids (VFAs) production increased by 9.98 % and 4.03 % under stearic acid and oleic acid loading, respectively. Acetic acid production increased by 20.66 % under stearic acid loading compared to the control group (CK). However, the LCFA stress restricted the degradation of solid organic matter, particularly under oleic acid stress. Analysis of microbial community structure and quorum sensing (QS) indicates that LCFA stress enhanced the relative abundance of Lactobacillus and Klebsiella. In QS system, the relative abundance of luxS declined from 0.157 % to 0.116 % and 0.125 % under oleic acid and stearic acid stress, respectively. LCFA stress limited the Autoinducer-2 (AI-2) biosynthesis, suggesting that microorganisms cannot use QS to resist the LCFA stress. Metagenomic sequencing showed that LCFA stress promoted acetic acid production via the conversion of pyruvate and acetyl-CoA to acetate. Direct conversion of pyruvate to acetic acid increased by 47.23 % compared to the CK group, accounting for the enhanced acetic acid production under stearic acid loading. The abundance of β-oxidation pathway under stearic acid loading was lower than under oleic acid loading. Overall, the stimulating direct conversion of pyruvate plays a pivotal role in enhancing acetic acid biosynthesis under stearic acid loading, providing insights into the effect of LCFA on mechanism of FW acidogenic fermentation.},
}
@article {pmid39151617,
year = {2024},
author = {Galisteo, C and Puente-Sánchez, F and de la Haba, RR and Bertilsson, S and Sánchez-Porro, C and Ventosa, A},
title = {Metagenomic insights into the prokaryotic communities of heavy metal-contaminated hypersaline soils.},
journal = {The Science of the total environment},
volume = {951},
number = {},
pages = {175497},
doi = {10.1016/j.scitotenv.2024.175497},
pmid = {39151617},
issn = {1879-1026},
mesh = {*Soil Microbiology ; *Metals, Heavy/analysis ; *Soil Pollutants/analysis ; *Bacteria/metabolism/classification ; *Microbiota ; *Archaea/genetics ; Soil/chemistry ; Spain ; Salinity ; Metagenome ; Metagenomics ; },
abstract = {Saline soils and their microbial communities have recently been studied in response to ongoing desertification of agricultural soils caused by anthropogenic impacts and climate change. Here we describe the prokaryotic microbiota of hypersaline soils in the Odiel Saltmarshes Natural Area of Southwest Spain. This region has been strongly affected by mining and industrial activity and feature high levels of certain heavy metals. We sequenced 18 shotgun metagenomes through Illumina NovaSeq from samples obtained from three different areas in 2020 and 2021. Taxogenomic analyses demonstrate that these soils harbored equal proportions of archaea and bacteria, with Methanobacteriota, Pseudomonadota, Bacteroidota, Gemmatimonadota, and Balneolota as most abundant phyla. Functions related to the transport of heavy metal outside the cytoplasm are among the most relevant features of the community (i.e., ZntA and CopA enzymes). They seem to be indispensable to avoid the increase of zinc and copper concentration inside the cell. Besides, the archaeal phylum Methanobacteriota is the main arsenic detoxifier within the microbiota although arsenic related genes are widely distributed in the community. Regarding the osmoregulation strategies, "salt-out" mechanism was identified in part of the bacterial population, whereas "salt-in" mechanism was present in both domains, Bacteria and Archaea. De novo biosynthesis of two of the most universal compatible solutes was detected, with predominance of glycine betaine biosynthesis (betAB genes) over ectoine (ectABC genes). Furthermore, doeABCD gene cluster related to the use of ectoine as carbon and energy source was solely identified in Pseudomonadota and Methanobacteriota.},
}
@article {pmid39151562,
year = {2024},
author = {Rahimian, M and Panahi, B},
title = {Metagenome sequence data mining for viral interaction studies: Review on progress and prospects.},
journal = {Virus research},
volume = {349},
number = {},
pages = {199450},
pmid = {39151562},
issn = {1872-7492},
mesh = {*Metagenomics/methods ; *Metagenome ; *Viruses/genetics/classification ; *Computational Biology/methods ; *Data Mining ; *High-Throughput Nucleotide Sequencing ; Humans ; Animals ; },
abstract = {Metagenomics has been greatly accelerated by the development of next-generation sequencing (NGS) technologies, which allow scientists to discover and describe novel microorganisms without the need for conventional culture techniques. Examining integrative bioinformatics methods used in viral interaction research, this study highlights metagenomic data from various contexts. Accurate viral identification depends on high-purity genetic material extraction, appropriate NGS platform selection, and sophisticated bioinformatics tools like VirPipe and VirFinder. The efficiency and precision of metagenomic analysis are further improved with the advent of AI-based techniques. The diversity and dynamics of viral communities are demonstrated by case studies from a variety of environments, emphasizing the seasonal and geographical variations that influence viral populations. In addition to speeding up the discovery of new viruses, metagenomics offers thorough understanding of virus-host interactions and their ecological effects. This review provides a promising framework for comprehending the complexity of viral communities and their interactions with hosts, highlighting the transformational potential of metagenomics and bioinformatics in viral research.},
}
@article {pmid39151360,
year = {2024},
author = {Ou, Y and Wu, M and Yu, Y and Liu, Z and Zhang, Y and Yi, N},
title = {Nitrogen utilization efficiency assessment during bioremediation of petroleum-contaminated loess soils: insights from metagenomic analysis.},
journal = {Journal of hazardous materials},
volume = {478},
number = {},
pages = {135506},
doi = {10.1016/j.jhazmat.2024.135506},
pmid = {39151360},
issn = {1873-3336},
mesh = {*Biodegradation, Environmental ; *Soil Pollutants/metabolism ; *Petroleum/metabolism ; *Nitrogen/metabolism ; *Soil Microbiology ; Hydrocarbons/metabolism ; Metagenomics ; },
abstract = {Nitrogen addition is commonly used to remediate total petroleum hydrocarbons (TPH) in petroleum-contaminated soils. However, acceptable exogenous nitrogen dosages and their utilization efficiency for the degradation of hydrocarbons in oil-polluted soils are not well understood. This study compared the hydrocarbon bioremediation capacity by applying different doses of NH4Cl as a stimulant in soils contaminated with TPH at 8553 and 17090 mg/kg. The results showed acceptable exogenous nitrogen levels ranging from 60 to 360 mg N/kg soil, and the optimal nitrogen dosage for TPH remediation was 136 mg N/kg in soils with different TPH concentrations. The nitrogen availability efficiency (NAE) and nitrogen polarization factor availability (NPFA) in the 136 mg N/kg addition treatments were 6.69 and 20.47 mg/mg in 8533 mg/kg TPH-polluted soil, and 6.03 and 31.11 mg/mg in 17090 mg/kg TPH-polluted soil, respectively. Metagenomic analysis revealed that the application of 136 mg/kg nitrogen facilitated ammonia oxidation and nitrite reduction to nitric oxide, and induced soil microorganisms to undergo regulatory or adaptive changes in energy supply and metabolic state, which could aid in restoring the ecological functions of petroleum-contaminated soils. These findings underscore that 136 mg/kg of nitrogen dosage application is optimal for remediation of petroleum-contaminated soils irrespective of the TPH concentrations. This exogenous nitrogen application dosage for TPH remediation aligns with the nitrogen requirements for crop growth in agriculture.},
}
@article {pmid39151267,
year = {2024},
author = {Yan, W and Bai, R and Zhang, Q and Jiang, Y and Chen, G and Zhang, Y and Wu, Y and Guo, X and Xiao, Y and Zhao, F},
title = {Metagenomic insights into ecological risk of antibiotic resistome and mobilome in riverine plastisphere under impact of urbanization.},
journal = {Environment international},
volume = {190},
number = {},
pages = {108946},
doi = {10.1016/j.envint.2024.108946},
pmid = {39151267},
issn = {1873-6750},
mesh = {*Urbanization ; *Rivers/microbiology/chemistry ; Humans ; Drug Resistance, Microbial/genetics ; Metagenomics ; Anti-Bacterial Agents/pharmacology ; Microplastics ; },
abstract = {Microplastics (MPs) are of increasing concern due to their role as reservoirs for antibiotic resistance genes (ARGs) and pathogens. To date, few studies have explored the influence of anthropogenic activities on ARGs and mobile genetic elements (MGEs) within various riverine MPs, in comparison to their natural counterparts. Here an in-situ incubation was conducted along heavily anthropogenically-impacted Houxi River to characterize the geographical pattern of antibiotic resistome, mobilome and pathogens inhabiting MPs- and leaf-biofilms. The metagenomics result showed a clear urbanization-driven profile in the distribution of ARGs, MGEs and pathogens, with their abundances sharply increasing 4.77 to 19.90 times from sparsely to densely populated regions. The significant correlation between human fecal marker crAssphage and ARG (R[2] = 0.67, P=0.003) indicated the influence of anthropogenic activity on ARG proliferation in plastisphere and natural leaf surfaces. And mantel tests and random forest analysis revealed the impact of 17 socio-environmental factors, e.g., population density, antibiotic concentrations, and pore volume of materials, on the dissemination of ARGs. Partial least squares-path modeling further unveiled that intensifying human activities not only directly boosted ARGs abundance but also exerted a comparable indirect impact on ARGs propagation. Furthermore, the polyvinylchloride plastisphere created a pathogen-friendly habitat, harboring higher abundances of ARGs and MGEs, while polylactic acid are not likely to serve as vectors for pathogens in river, with a lower resistome risk score than that in leaf-biofilms. This study highlights the diverse ecological risks associated with the dissemination of ARGs and pathogens in varied MPs, offering insights for the policymaking of usage and control of plastics within urbanization.},
}
@article {pmid39151014,
year = {2024},
author = {Schickele, A and Debeljak, P and Ayata, SD and Bittner, L and Pelletier, E and Guidi, L and Irisson, JO},
title = {The genomic potential of photosynthesis in piconanoplankton is functionally redundant but taxonomically structured at a global scale.},
journal = {Science advances},
volume = {10},
number = {33},
pages = {eadl0534},
pmid = {39151014},
issn = {2375-2548},
mesh = {*Photosynthesis/genetics ; *Ribulose-Bisphosphate Carboxylase/genetics/metabolism ; Plankton/genetics/metabolism ; Genomics/methods ; Phylogeny ; Carbon Cycle ; Metagenomics/methods ; Metagenome ; Seawater ; },
abstract = {Carbon fixation is a key metabolic function shaping marine life, but the underlying taxonomic and functional diversity involved is only partially understood. Using metagenomic resources targeted at marine piconanoplankton, we provide a reproducible machine learning framework to derive the potential biogeography of genomic functions through the multi-output regression of gene read counts on environmental climatologies. Leveraging the Marine Atlas of Tara Oceans Unigenes, we investigate the genomic potential of primary production in the global ocean. The latter is performed by ribulose-1,5-bisphosphate carboxylase/oxygenase (RUBISCO) and is often associated with carbon concentration mechanisms in piconanoplankton, major marine unicellular photosynthetic organisms. We show that the genomic potential supporting C4 enzymes and RUBISCO exhibits strong functional redundancy and important affinity toward tropical oligotrophic waters. This redundancy is taxonomically structured by the dominance of Mamiellophyceae and Prymnesiophyceae in mid and high latitudes. These findings enhance our understanding of the relationship between functional and taxonomic diversity of microorganisms and environmental drivers of key biogeochemical cycles.},
}
@article {pmid39150994,
year = {2024},
author = {Malham, M and Vestergaard, MV and Bataillon, T and Villesen, P and Dempfle, A and Bang, C and Engsbro, AL and Jakobsen, C and Franke, A and Wewer, V and Thingholm, LB and Petersen, AM},
title = {The Composition of the Fecal and Mucosa-adherent Microbiota Varies Based on Age and Disease Activity in Ulcerative Colitis.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izae179},
pmid = {39150994},
issn = {1536-4844},
support = {//Aage and Johann Louis-Hansens Foundation/ ; //Aase and Ejnar Danielsens Foundation/ ; //German Research Foundation/ ; },
abstract = {BACKGROUND: Pediatric-onset ulcerative colitis (pUC) represents a more aggressive disease phenotype compared with adult-onset UC. We hypothesized that this difference can, in part, be explained by the composition of the microbiota.<br><br>METHODS: In a prospective, longitudinal study, we included pediatric (N&#x2005;=&#x2005;30) and adult (N&#x2005;=&#x2005;30) patients with newly or previously (>1 year) diagnosed UC. We analyzed the microbiota composition in the mucosa-adherent microbiota at baseline, using 16S rRNA gene sequencing, and the fecal microbiota at baseline and at 3-month intervals, using shotgun metagenomics.<br><br>RESULTS: For fecal samples, the bacterial composition differed between pUC and aUC in newly diagnosed patients (&#x3b2;-diversity, Bray Curtis: R2&#x2005;=&#x2005;0.08, P&#x2005;=&#x2005;.02). In colon biopsies, microbial diversity was higher in aUC compared with pUC (&#x3b1;-diversity, Shannon: estimated difference 0.54, P&#x2005;=&#x2005;.006). In the mucosa-adherent microbiota, Alistipes finegoldii was negatively associated with disease activity in pUC while being positively associated in aUC (estimate: -0.255 and 0.098, P&#x2005;=&#x2005;.003 and P&#x2005;=&#x2005;.02 in pUC and aUC, respectively). Finally, we showed reduced stability of the fecal microbiota in pediatric patients, evidenced by a different composition of the fecal microbiota in newly and previously diagnosed pUC, a pattern not found in adults.<br><br>CONCLUSIONS: Our results indicate that pediatric UC patients have a more unstable fecal microbiota and a lower &#x3b1; diversity than adult patients and that the microbiota composition differs between aUC and pUC patients. These findings offer some explanation for the observed differences between pUC and aUC and indicate that individualized approaches are needed if microbiota modifications are to be used in the future treatment of UC.},
}
@article {pmid39150770,
year = {2024},
author = {},
title = {Correction to: A novel bioinformatic method for the identification of antimicrobial peptides in metagenomes.},
journal = {Journal of applied microbiology},
volume = {135},
number = {8},
pages = {},
doi = {10.1093/jambio/lxae207},
pmid = {39150770},
issn = {1365-2672},
}
@article {pmid39150504,
year = {2024},
author = {Sessa, R and Filardo, S and Viscardi, MF and Brandolino, G and Muzii, L and Di Pietro, M and Porpora, MG},
title = {Characterization of the vaginal microbiota in Italian women with endometriosis: preliminary study.},
journal = {Archives of gynecology and obstetrics},
volume = {310},
number = {4},
pages = {2141-2151},
pmid = {39150504},
issn = {1432-0711},
mesh = {Humans ; Female ; *Endometriosis/microbiology ; Adult ; *Vagina/microbiology ; Cross-Sectional Studies ; Italy ; *Microbiota ; Young Adult ; Dysbiosis/microbiology ; Bacteria/isolation &amp; purification/classification/genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {PURPOSE: This cross-sectional study aims to assess the interplay between the vaginal microbiota and endometriosis.<br><br>METHODS: 123 consecutive Italian fertile women, aged between 20 and 40&#xa0;years old, were enrolled during a routine gynecological consultation; 24 were diagnosed with endometriosis and 99 did not complain of any gynecological disease. All women underwent a vaginal swab for the evaluation of the composition and diversity of vaginal microbiota by means of 16&#xa0;s rDNA metagenomic sequencing.<br><br>RESULTS: Compared to women with no gynecological disease, the vaginal microbiota in women with endometriosis showed a similar abundance of Lactobacillus spp.; however, a statistically significant lower abundance in the genera Pseudomonas (p&#x2009;<&#x2009;0.01), Bifidobacterium (p&#x2009;<&#x2009;0.05), Novispirillum (p&#x2009;<&#x2009;0.0000001) and Sphingomonas (p&#x2009;<&#x2009;0.0000001), and a statistically significant increase in the abundance of the genera Escherichia (p&#x2009;<&#x2009;0.00001), Megasphaera (p&#x2009;<&#x2009;0.00001), and Sneathia (p&#x2009;<&#x2009;0.0001) were observed.<br><br>CONCLUSIONS: There is a complex interplay between vaginal microbiota composition and endometriosis, showing a distinct microbial signature in the bacterial genera usually found in dysbiosis.},
}
@article {pmid39150251,
year = {2024},
author = {Lv, Y and Zhen, C and Liu, A and Hu, Y and Yang, G and Xu, C and Lou, Y and Cheng, Q and Luo, Y and Yu, J and Fang, Y and Zhao, H and Peng, K and Yu, Y and Lou, J and Chen, J and Ni, Y},
title = {Profiles and interactions of gut microbiome and intestinal microRNAs in pediatric Crohn's disease.},
journal = {mSystems},
volume = {9},
number = {9},
pages = {e0078324},
pmid = {39150251},
issn = {2379-5077},
mesh = {Humans ; *MicroRNAs/genetics/metabolism ; *Crohn Disease/microbiology/genetics/metabolism ; *Gastrointestinal Microbiome ; Child ; Male ; Female ; Adolescent ; Feces/microbiology ; Dysbiosis/genetics/microbiology ; Intestines/microbiology ; Bacteria/genetics/isolation &amp; purification ; Intestinal Mucosa/microbiology/metabolism ; },
abstract = {UNLABELLED: Gut dysbiosis is closely related to dysregulated microRNAs (miRNAs) in the intestinal epithelial cells, which plays an important role in the pathogenesis of Crohn's disease (CD). We investigated the relationship between fecal gut microbiome (GM) and intestinal tissue miRNAs in different stages of pediatric CD. Metagenomic analysis and miRNA sequencing were conducted to examine the GM and intestinal miRNA profiles of CD patients before and after clinical induction therapy and the controls. Twenty-seven newly diagnosed, therapy-naïve pediatric patients with active CD and 11 non-inflammatory bowel disease (IBD) controls were recruited in this study. Among CD patients, 11 patients completed induction treatment and reached clinical remission. Both GM and miRNA profiles were significantly changed between CD patients and controls. Seven key bacteria were identified at species level including Defluviitalea raffinosedens, Thermotalea metallivorans, Roseburia intestinalis, Dorea sp. AGR2135, Escherichia coli, Shigella sonnei, and Salmonella enterica, the exact proportions of which were further validated by real-time quantitative PCR analysis. Eight key miRNAs were also identified including hsa-miR-215-5p, hsa-miR-194-5p, hsa-miR-12135, hsa-miR-509-3-5p, hsa-miR-212-5p, hsa-miR-4448, hsa-miR-501-3p, and hsa-miR-503-5p. The functional enrichment analysis of differential miRNAs indicated the significantly altered cyclin protein, cyclin-dependent protein, and cell cycle pathway. The close interactions between seven key bacteria and eight key miRNAs were further investigated by miRNA target prediction. The association between specific miRNA expressions and key gut bacteria at different stages of CD supported their important roles as potential molecular biomarkers. Understanding the relationship between them will help us to explore the molecular mechanisms of CD.<br><br>IMPORTANCE: Since previous studies have focused on the change of the fecal gut microbiome and intestinal tissue miRNA in pediatric Crohn's disease (CD), the relationship between them in different stages is still not clear. This is the first study to explore the gut microbiota and miRNA and their correlations with the Pediatric Crohn's Disease Activity Index (PCDAI). Crohn's Disease Endoscopic Index of Severity (CDEIS), and calprotectin, by applying two omics approach in three different groups (active CD, CD in remission with exclusive enteral nutrition or infliximab induction therapy, and the healthy controls). Both gut microbiome structure and the miRNA profiles were significantly changed in the different stage of CD. Seven key gut microbiome at species and eight key miRNAs were found, and their close interactions were further fully investigated by miRNA target prediction.},
}
@article {pmid39149810,
year = {2024},
author = {Liu, J and Wang, WJ and Xu, GF and Wang, YX and Lin, Y and Zheng, X and Yao, SH and Zheng, KH},
title = {Does Microbiome Contribute to Longevity? Compositional and Functional Differences in Gut Microbiota in Chinese Long-Living (&gt;90 Years) and Elderly (65-74 Years) Adults.},
journal = {Omics : a journal of integrative biology},
volume = {28},
number = {9},
pages = {461-469},
doi = {10.1089/omi.2024.0120},
pmid = {39149810},
issn = {1557-8100},
mesh = {Humans ; Aged ; *Longevity ; *Gastrointestinal Microbiome/physiology ; Aged, 80 and over ; Male ; Female ; China ; Bacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; East Asian People ; },
abstract = {The study of longevity and its determinants has been revitalized with the rise of microbiome scholarship. The gut microbiota have been established to play essential protective, metabolic, and physiological roles in human health and disease. The gut dysbiosis has been identified as an important factor contributing to the development of multiple diseases. Accordingly, it is reasonable to hypothesize that the gut microbiota of long-living individuals have healthy antiaging-associated gut microbes, which, by extension, might provide specific molecular targets for antiaging treatments and interventions. In the present study, we compared the gut microbiota of Chinese individuals in two different age groups, long-living adults (aged over 90 years) and elderly adults (aged 65-74 years) who were free of major diseases. We found significantly lower relative abundances of bacteria in the genera Sutterella and Megamonas in the long-living individuals. Furthermore, we established that while biological processes such as autophagy (GO:0006914) and telomere maintenance through semiconservative replication (GO:0032201) were enhanced in the long-living group, response to lipopolysaccharide (GO:0032496), nicotinamide adenine dinucleotide oxidation (GO:0006116), and S-adenosyl methionine metabolism (GO:0046500) were weakened. Moreover, the two groups were found to differ with respect to amino acid metabolism. We suggest that these compositional and functional differences in the gut microbiota may potentially be associated with mechanisms that contribute to determining longevity or aging.},
}
@article {pmid39149494,
year = {2024},
author = {Lewis, ZJ and Scott, A and Madden, C and Vik, D and Zayed, AA and Smith, GJ and Justice, SS and Rudinsky, A and Hokamp, J and Hale, VL},
title = {Evaluating urine volume and host depletion methods to enable genome-resolved metagenomics of the urobiome.},
journal = {Research square},
volume = {},
number = {},
pages = {},
pmid = {39149494},
issn = {2693-5015},
support = {K08 ES034821/ES/NIEHS NIH HHS/United States ; },
abstract = {BACKGROUND: The gut microbiome has emerged as a clear player in health and disease, in part by mediating host response to environment and lifestyle. The urobiome (microbiota of the urinary tract) likely functions similarly. However, efforts to characterize the urobiome and assess its functional potential have been limited due to technical challenges including low microbial biomass and high host cell shedding in urine. Here, to begin addressing these challenges, we evaluate urine sample volume (100 ml - 5 mL), and host DNA depletion methods and their effects on urobiome profiles in healthy dogs, which are a robust large animal model for the human urobiome. We collected urine from seven dogs and fractionated samples into aliquots. One set of samples was spiked with host (canine) cells to model a biologically relevant host cell burden in urine. Samples then underwent DNA extraction followed by 16S rRNA gene and shotgun metagenomic sequencing. We then assembled metagenome assembled genomes (MAGs) and compared microbial composition and diversity across groups. We tested six methods of DNA extraction: QIAamp BiOstic Bacteremia (no host depletion), QIAamp DNA Microbiome, Molzym MolYsis, NEBNext Microbiome DNA Enrichment, Zymo HostZERO, and Propidium Monoazide.<br><br>RESULTS: In relation to urine sample volume, [3] 3.0 mL resulted in the most consistent urobiome profiling. In relation to host depletion, individual (dog) but not extraction method drove overall differences in microbial composition. DNA Microbiome yielded the greatest microbial diversity in 16S rRNA sequencing data and shotgun metagenomic sequencing data, and maximized MAG recovery while effectively depleting host DNA in host-spiked urine samples. As proof-of-principle, we then mined MAGs for core metabolic functions and environmental chemical metabolism. We identified long chain alkane utilization in two of the urine MAGs. Long chain alkanes are common pollutants that result from industrial combustion processes and end up in urine.<br><br>CONCLUSIONS: This is the first study, to our knowledge, to demonstrate environmental chemical degradation potential in urine microbes through genome-resolved metagenomics. These findings provide guidelines for studying the urobiome in relation to sample volume and host depletion, and lay the foundation for future evaluation of urobiome function in relation to health and disease.},
}
@article {pmid39149418,
year = {2024},
author = {Zhang, J and Gao, L and Zhu, C and Jin, J and Song, C and Dong, H and Li, Z and Wang, Z and Chen, Y and Yang, Z and Tan, Y and Wang, L},
title = {Corrigendum: Clinical value of metagenomic next-generation sequencing by Illumina and Nanopore for the detection of pathogens in bronchoalveolar lavage fluid in suspected community-acquired pneumonia patients.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1468511},
doi = {10.3389/fcimb.2024.1468511},
pmid = {39149418},
issn = {2235-2988},
abstract = {[This corrects the article DOI: 10.3389/fcimb.2022.1021320.].},
}
@article {pmid39149354,
year = {2024},
author = {Heber, K and Tian, S and Betancurt-Anzola, D and Koo, H and Bisanz, JE},
title = {StrainR2 accurately deconvolutes strain-level abundances in synthetic microbial communities.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39149354},
issn = {2692-8205},
support = {R00 AI147165/AI/NIAID NIH HHS/United States ; R35 GM151045/GM/NIGMS NIH HHS/United States ; },
abstract = {BACKGROUND: Synthetic microbial communities offer an opportunity to conduct reductionist research in tractable model systems. However, deriving abundances of highly related strains within these communities is currently unreliable. 16S rRNA gene sequencing does not resolve abundance at the strain level, standard methods for analysis of shotgun metagenomic sequencing do not account for ambiguous mapping between closely related strains, and other methods such as quantitative PCR (qPCR) scale poorly and are resource prohibitive for complex communities. We present StrainR2, which utilizes shotgun metagenomic sequencing paired with a k-mer-based normalization strategy to provide high accuracy strain-level abundances for all members of a synthetic community, provided their genomes.<br><br>RESULTS: Both in silico, and using sequencing data derived from gnotobiotic mice colonized with a synthetic fecal microbiota, StrainR2 resolves strain abundances with greater accuracy than other tools utilizing shotgun metagenomic sequencing reads and can resolve complex mixtures of highly related strains. Through experimental validation and benchmarking, we demonstrate that StrainR2's accuracy is comparable to that of qPCR on a subset of strains resolved using absolute quantification. Further, it is capable of scaling to communities of hundreds of strains and efficiently utilizes memory being capable of running both on personal computers and high-performance computing nodes.<br><br>CONCLUSIONS: Using shotgun metagenomic sequencing reads is a viable method for determining accurate strain-level abundances in synthetic communities using StrainR2.},
}
@article {pmid39148859,
year = {2024},
author = {Sumner, JT and Pickens, CI and Huttelmaier, S and Moghadam, AA and Abdala-Valencia, H and , and Hauser, AR and Seed, PC and Wunderink, RG and Hartmann, EM},
title = {Transitions in lung microbiota landscape associate with distinct patterns of pneumonia progression.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
pmid = {39148859},
support = {R01 HL153122/HL/NHLBI NIH HHS/United States ; U19 AI181102/AI/NIAID NIH HHS/United States ; U19 AI135964/AI/NIAID NIH HHS/United States ; P01 HL154998/HL/NHLBI NIH HHS/United States ; R01 HL149883/HL/NHLBI NIH HHS/United States ; },
abstract = {Pneumonia and other lower respiratory tract infections are the leading contributors to global mortality of any communicable disease [1]. During normal pulmonary homeostasis, competing microbial immigration and elimination produce a transient microbiome with distinct microbial states [2-4]. Disruption of underlying ecological forces, like aspiration rate and immune tone, are hypothesized to drive microbiome dysbiosis and pneumonia progression [5-7]. However, the precise microbiome transitions that accompany clinical outcomes in severe pneumonia are unknown. Here, we leverage our unique systematic and serial bronchoscopic sampling to combine quantitative PCR and culture for bacterial biomass with 16S rRNA gene amplicon, shotgun metagenomic, and transcriptomic sequencing in patients with suspected pneumonia to distill microbial signatures of clinical outcome. These data support the presence of four distinct microbiota states-oral-like, skin-like, Staphylococcus-predominant, and mixed-each differentially associated with pneumonia subtype and responses to pneumonia therapy. Infection-specific dysbiosis, quantified relative to non-pneumonia patients, associates with bacterial biomass and elevated oral-associated microbiota. Time series analysis suggests that microbiome shifts from baseline are greater with successful pneumonia therapy, following distinct trajectories dependent on the pneumonia subtype. In summary, our results highlight the dynamic nature of the lung microbiome as it progresses through community assemblages that parallel patient prognosis. Application of a microbial ecology framework to study lower respiratory tract infections enables contextualization of the microbiome composition and gene content within clinical phenotypes. Further unveiling the ecological dynamics of the lung microbial ecosystem provides critical insights for future work toward improving pneumonia therapy.},
}
@article {pmid39148686,
year = {2024},
author = {Oki, H and Niwa, R and Pranee, S and Motooka, D and Onda, Y and Nakata, J and Nakajima, H and Oka, Y and Sugiyama, H and Yoshii, Y and Anzai, N and Nakamura, S and Iida, T},
title = {Identification of causative fungus from sterile abscess using metagenomics followed by in situ hybridization.},
journal = {Access microbiology},
volume = {6},
number = {8},
pages = {},
pmid = {39148686},
issn = {2516-8290},
abstract = {Introduction. Invasive fungal infections require early diagnosis for treatment. Microscopic observation of biopsy and blood culture is the gold standard for the identification of the causative fungus, but it is difficult to identify the causative pathogen by a sterile abscess biopsy. Case Presentation. We present a case report of breakthrough invasive trichosporonosis in a 65-year-old Japanese male with acute myeloid leukaemia receiving antifungal prophylaxis. Blood cultures showed no fungal growth, and a liver biopsy and a removed spleen with abscess showed fragmented fungi, but no fungal identification was possible. This report demonstrates that retrospective analyses were able to identify the causative fungus. Conclusion. We narrowed down the candidate fungi by deep sequencing of the ITS1 region of fungal genome and confirmed that the fungus observed in the specimen was Trichosporon asahii by in situ hybridization using a DNA probe targeting 26S rRNA.},
}
@article {pmid39147851,
year = {2024},
author = {Földvári, G and Tauber, Z and Tóth, GE and Cadar, D and Bialonski, A and Horváth, B and Szabó, &#xc9; and Lanszki, Z and Zana, B and Varga, Z and Földes, F and Kemenesi, G},
title = {Genomic characterization of Volzhskoe tick virus (Bunyaviricetes) from a Hyalomma marginatum tick, Hungary.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {18945},
pmid = {39147851},
issn = {2045-2322},
support = {CA21170//COST/ ; CA21170//COST/ ; CA21170//COST/ ; RRF-2.3.1-21-2022-00006//National Research, Development and Innovation Office/ ; RRF-2.3.1-21-2022-00006//National Research, Development and Innovation Office/ ; RRF-2.3.1-21-2022-00006//National Research, Development and Innovation Office/ ; RRF-2.3.1-21-2022-00006//National Research, Development and Innovation Office/ ; RRF-2.3.1-21-2022-00006//National Research, Development and Innovation Office/ ; RRF-2.3.1-21-2022-00006//National Research, Development and Innovation Office/ ; RRF-2.3.1-21-2022-00006//National Research, Development and Innovation Office/ ; RRF-2.3.1-21-2022-00006//National Research, Development and Innovation Office/ ; RRF-2.3.1-21-2022-00006//National Research, Development and Innovation Office/ ; RRF-2.3.1-21-2022-00006//National Research, Development and Innovation Office/ ; 13N15449//German Federal Ministry of Education and Research/ ; 13N15449//German Federal Ministry of Education and Research/ ; },
mesh = {Animals ; Hungary ; *Phylogeny ; *Genome, Viral ; Ixodidae/virology ; Ticks/virology ; Genomics/methods ; Metagenomics/methods ; },
abstract = {Hyalomma marginatum, a vector for the high-consequence pathogen, the Crimean-Congo hemorrhagic fever virus (CCHFV), needs particular attention due to its impact on public health. Although it is a known vector for CCHFV, its general virome is largely unexplored. Here, we report findings from a citizen science monitoring program aimed to understand the prevalence and diversity of tick-borne pathogens, particularly focusing on Hyalomma ticks in Hungary. In 2021, we identified one adult specimen of Hyalomma marginatum and subjected it to Illumina-based viral metagenomic sequencing. Our analysis revealed sequences of the uncharacterized Volzhskoe tick virus, an unclassified member of the class Bunyaviricetes. The in silico analysis uncovered key genetic regions, including the glycoprotein and the RNA-dependent RNA polymerase (RdRp) coding regions. Phylogenetic analysis indicated a close relationship between our Volzhskoe tick virus sequences and other unclassified Bunyaviricetes species. These related species of unclassified Bunyaviricetes were detected in vastly different geolocations. These findings highlight the remarkable diversity of tick specific viruses and emphasize the need for further research to understand the transmissibility, seroreactivity or the potential pathogenicity of Volzhskoe tick virus and related species.},
}
@article {pmid39147792,
year = {2024},
author = {Zhang, Y and Jing, H},
title = {Metagenome sequencing and 107 microbial genomes from seamount sediments along the Yap and Mariana trenches.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {887},
pmid = {39147792},
issn = {2052-4463},
mesh = {*Metagenome ; *Geologic Sediments/microbiology ; *Phylogeny ; *Bacteria/genetics/classification ; *Archaea/genetics ; Genome, Microbial ; Genome, Archaeal ; Genome, Bacterial ; },
abstract = {Microbes in the sediments across a series of seamounts along the island arc of the Yap and Mariana trenches were investigated by metagenome. In this study, we reconstructed 107 metagenome-assembled genomes (MAGs), including 100 bacteria and 7 archaea. All the MAGs exhibited >75% completeness and <10% contamination, with 26 MAGs being classified as 'nearly complete' (completeness >90%), while 50 falling within 80-90% range and 31 between 75-80% complete. Phylogenomic analysis revealed that 86% (n = 92) of these MAGs represented new taxa at different taxonomical levels. The species composition of these MAGs was most consistent with the previous reports, with the most abundant phyla being Proteobacteria (n = 39), Methylomirabilota (n = 27), and Nitrospirota (n = 7). These draft genomes provided novel data on species diversity and function in the seamount microbial community, which will provide reference data for extensive comparative genomic studies across crucial phylogenetic groups worldwide.},
}
@article {pmid39147529,
year = {2024},
author = {Xiang, L and Zhuo, S and Luo, W and Tian, C and Xu, S and Li, X and Zhu, Y and Feng, R and Chen, M},
title = {Decoding polyphenol metabolism in patients with Crohn's disease: Insights from diet, gut microbiota, and metabolites.},
journal = {Food research international (Ottawa, Ont.)},
volume = {192},
number = {},
pages = {114852},
doi = {10.1016/j.foodres.2024.114852},
pmid = {39147529},
issn = {1873-7145},
mesh = {Humans ; *Crohn Disease/microbiology/metabolism/drug therapy ; *Gastrointestinal Microbiome/physiology ; *Polyphenols/metabolism ; Female ; Male ; Adult ; *Diet ; Hippurates/metabolism ; Middle Aged ; Young Adult ; Bacteria/classification/metabolism/genetics ; Feces/microbiology ; },
abstract = {Crohn's disease (CD) is a chronic and progressive inflammatory disease that can involve any part of the gastrointestinal tract. The protective role of dietary polyphenols has been documented in preclinical models of CD. Gut microbiota mediates the metabolism of polyphenols and affects their bioactivity and physiological functions. However, it remains elusive the capacity of microbial polyphenol metabolism in CD patients and healthy controls (HCs) along with its correlation with polyphenols intake and polyphenol-derived metabolites. Thus, we aimed to decode polyphenol metabolism in CD patients through aspects of diet, gut microbiota, and metabolites. Dietary intake analysis revealed that CD patients exhibited decreased intake of polyphenols. Using metagenomic data from two independent clinical cohorts (FAH-SYSU and PRISM), we quantified abundance of polyphenol degradation associated bacteria and functional genes in CD and HCs and observed a lower capacity of flavonoids degradation in gut microbiota residing in CD patients. Furthermore, through analysis of serum metabolites and enterotypes in participants of FAH-SYSU cohort, we observed that CD patients exhibited reduced levels of serum hippuric acid (HA), one of polyphenol-derived metabolites. HA level was higher in healthier enterotypes (characterized by dominance of Ruminococcaceae and Prevotellaceae, dominant by HCs) and positively correlated with multiple polyphenols intake and abundance of bacteria engaged in flavonoids degradation as well as short-chain fatty acid production, which could serve as a biomarker for effective polyphenol metabolism by the gut microbiota and a healthier gut microbial community structure. Overall, our findings provide a foundation for future work exploring the polyphenol-based or microbiota-targeted therapeutic strategies in CD.},
}
@article {pmid39147499,
year = {2024},
author = {Magliulo, R and Valentino, V and Balivo, A and Esposito, A and Genovese, A and Ercolini, D and De Filippis, F},
title = {Microbiome signatures associated with flavor development differentiate Protected Designation of origin water Buffalo Mozzarella cheese from different production areas.},
journal = {Food research international (Ottawa, Ont.)},
volume = {192},
number = {},
pages = {114798},
doi = {10.1016/j.foodres.2024.114798},
pmid = {39147499},
issn = {1873-7145},
mesh = {*Cheese/microbiology/analysis ; Animals ; *Volatile Organic Compounds/analysis ; *Microbiota ; *Buffaloes ; Italy ; *Gas Chromatography-Mass Spectrometry ; *Taste ; Food Microbiology ; Lactobacillus helveticus ; Streptococcus thermophilus/classification ; },
abstract = {Water Buffalo Mozzarella (BM) is a typical cheese from Southern Italy with unique flavor profile and texture. It is produced following a traditional back-slopping procedure and received the Protected Designation of Origin (PDO) label. To better understand the link between the production area, the microbiome composition and the flavor profile of the products, we performed a multiomic characterization of PDO BM collected from 57 different dairies located in the two main PDO production area, i.e. Caserta (n = 35) and Salerno (n = 22). Thus, we assessed the microbiome by high-throughput shotgun metagenomic sequencing and the Volatile Organic Compounds (VOCs) by gas chromatography/mass spectrometry (GC/MS). Streptococcus thermophilus, Lactobacillus helveticus, and Lactobacillus delbrueckii subsp. delbrueckii were identified as the core microbiome present in all samples. However, the microbiome taxonomic profiles resulted in a clustering of the samples based on their geographical origin, also showing that BM from Caserta had a greater microbial diversity. Consistently, Caserta and Salerno samples also showed different VOC profiles. These results suggest that the microbiome and its specific metabolic activity are part of the terroir that shape BM specific features, linking this traditional product with the area of production, thus opening new clues for improving traceability and fraud protection of traditional products.},
}
@article {pmid39147372,
year = {2024},
author = {Jara-Servin, A and Mejia, G and Romero, MF and Peimbert, M and Alcaraz, LD},
title = {Unravelling the genomic and environmental diversity of the ubiquitous Solirubrobacter.},
journal = {Environmental microbiology},
volume = {26},
number = {8},
pages = {e16685},
doi = {10.1111/1462-2920.16685},
pmid = {39147372},
issn = {1462-2920},
support = {CVU 725278//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; IN206824//Universidad Nacional Aut&#xf3;noma de M&#xe9;xico, DGAPA-PAPIIT-UNAM/ ; },
mesh = {*Soil Microbiology ; *Phylogeny ; *Genome, Bacterial ; *RNA, Ribosomal, 16S/genetics ; Rhizosphere ; Genomics ; Metagenomics ; Genetic Variation ; },
abstract = {Solirubrobacter, though widespread in soils and rhizospheres, has been relatively unexplored despite its ubiquity. Previously acknowledged as a common soil bacterium, our research explores its phylogenomics, pangenomics, environmental diversity, and interactions within bacterial communities. By analysing seven genomic sequences, we have identified a pangenome consisting of 19,645 protein families, of which 2644 are shared across all studied genomes, forming the core genome. Interestingly, despite the non-motility of reported isolates, we discovered genes for flagellin and a partial flagellum assembly pathway. Examining the 16S ribosomal RNA genes of Solirubrobacter revealed substantial diversity, with 3166 operational taxonomic units identified in Mexican soils. Co-occurrence network analysis further demonstrated its significant integration within bacterial communities. Through phylogenomic scrutiny, we conclusively excluded the NCBI's GCA_009993245.1 genome from being classified as a Solirubrobacter. Our research into the metagenomic diversity of Solirubrobacter across various environments confirmed its presence in rhizospheres and certain soils, underscoring its adaptability. The geographical ubiquity of Solirubrobacter in rhizospheres raises intriguing questions regarding its potential interactions with plant hosts and the biotic and abiotic factors influencing its presence in soil. Given its ecological significance and genetic diversity, Solirubrobacter warrants further investigation as a potentially crucial yet underappreciated keystone species.},
}
@article {pmid39147334,
year = {2024},
author = {Hu, Z and Yao, Y and Chen, F and Feng, L and Yuan, Z and Deng, J and Huang, L and Yin, Y and Tang, X},
title = {Integrated analyses of the intestinal microbiome and transcriptome in Ningxiang piglets.},
journal = {Genomics},
volume = {116},
number = {5},
pages = {110919},
doi = {10.1016/j.ygeno.2024.110919},
pmid = {39147334},
issn = {1089-8646},
abstract = {Ningxiang (NX) pig has been recognized as one of the most famous Chinese indigenous breeds due to its characteristics in stress resistance. However, intestinal microbial feature and gene profiling in NX piglets have not been studied. Here, we compared the intestinal microbiome and transcriptome between NX and Duroc × Landrace × Large white (DLY) piglets and found the high enrichment of several colonic Bacteroides, Prevotella and Clostridium species in NX piglets. Further functional analyses revealed their predominant function in methane, glycolysis and gluconeogenesis metabolism. Our mRNA-sequencing data unraveled the distinct colonic gene expression between these two breeds. In particular, we showed that the improved intestinal function in NX piglets may be determined by enhanced intestinal barrier gene expression and varied immune gene expression through modulating the composition of the gut microbes. Together, our study revealed the intestinal characteristics of NX piglets, providing their potential application in improving breeding strategies and developing dietary interventions.},
}
@article {pmid39147284,
year = {2024},
author = {Zhang, D and Yang, A and Sheng, K and Fang, S and Zhou, L},
title = {Application of the second-generation sequencing technology of metagenomics in the detection of pathogens in respiratory patients.},
journal = {Journal of microbiological methods},
volume = {225},
number = {},
pages = {107021},
doi = {10.1016/j.mimet.2024.107021},
pmid = {39147284},
issn = {1872-8359},
mesh = {Humans ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; Retrospective Studies ; *Bacteria/isolation &amp; purification/genetics/classification ; Male ; Middle Aged ; Female ; *Respiratory Tract Infections/microbiology/diagnosis/virology ; *Fungi/isolation &amp; purification/genetics/classification ; Aged ; Adult ; Viruses/isolation &amp; purification/genetics/classification ; China ; Sensitivity and Specificity ; Aged, 80 and over ; },
abstract = {OBJECTIVE: To explore the application value of the second-generation metagenomic next-generation sequencing (mNGS) in the detection of pathogens in patients with pulmonary infection.<br><br>METHODS: We conducted a retrospective analysis of 65 pulmonary infection cases treated at our institution and the Fifth People's Hospital of Shanghai between January 2021 and May 2023. All subjects were subjected to mNGS, targeted next-generation sequencing (tNGS), and conventional microbiological culture. A comparative analysis was performed to evaluate the diversity and quantity of pathogens identified by these methodologies and to appraise their respective diagnostic capabilities in pulmonary infection diagnostics.<br><br>RESULTS: The mNGS successfully identified etiological agents in 60 of the 65 cases, compared to tNGS, which yielded positive results in 42 cases, and conventional laboratory cultures, which detected pathogens in 24 cases. At the bacterial genus level, mNGS discerned 9 genera, 11 species, and 92 isolates of pathogenic bacteria, whereas tNGS identified 8 genera, 8 species, and 71 isolates. Conventional methods were less sensitive, detecting only 6 genera, 7 species, and 33 isolates. In terms of fungal detection, mNGS identified 4 fungal species, tNGS detected 4 isolates of the Candida genus, and conventional methods identified 2 isolates of the same genus. Viral detection at the species level revealed 10 species and 46 isolates by mNGS, whereas tNGS detected only 3 species and 7 isolates. The area under the receiver operating characteristic curve (AUC) with 95% confidence intervals for diagnosing pulmonary infections was 0.818 (0.671 to 0.966) for mNGS, 0.668 (0.475 to 0.860) for tNGS, and 0.721 (0.545 to 0.897) for conventional culture.The mNGS demonstrates superior diagnostic efficacy and pathogen detection breadth in critically ill patients with respiratory infections, offering a significant advantage by reducing the time to diagnosis. The enhanced sensitivity and comprehensive pathogen profiling of mNGS underscore its potential as a leading diagnostic tool in clinical microbiology.},
}
@article {pmid39147198,
year = {2024},
author = {Zeng, Y and Guo, M and Wu, Q and Tan, X and Jiang, C and Teng, F and Chen, J and Zhang, F and Ma, X and Li, X and Gu, J and Huang, W and Zhang, C and Yuen-Kwan Law, B and Long, Y and Xu, Y},
title = {Gut microbiota-derived indole-3-propionic acid alleviates diabetic kidney disease through its mitochondrial protective effect via reducing ubiquitination mediated-degradation of SIRT1.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2024.08.018},
pmid = {39147198},
issn = {2090-1224},
abstract = {INTRODUCTION: Gut microbes and their metabolites play crucial roles in the pathogenesis of diabetic kidney disease (DKD). However, which one and how specific gut-derived metabolites affect the progression of DKD remain largely unknown.<br><br>OBJECTIVES: This study aimed to investigate the potential roles of indole-3-propionic acid (IPA), a microbial metabolite of tryptophan, in DKD.<br><br>METHODS: Metagenomic sequencing was performed to analyze the microbiome structure in DKD. Metabolomics screening and validation were conducted to identify characteristic metabolites associated with DKD. The protective effect of IPA on DKD glomerular endothelial cells (GECs) was assessed through in vivo and in vitro experiments. Further validation via western blot, immunoprecipitation, gene knockout, and site-directed mutation elucidated the mechanism of IPA on mitochondrial injury.<br><br>RESULTS: Alterations in gut microbial community structure and dysregulated tryptophan metabolism were evident in DKD mice. Serum IPA levels were significantly reduced in DKD patients and correlated with fasting blood glucose, HbA1c, urine albumin-to-creatinine ratio (UACR), and estimated glomerular filtration rate (eGFR). IPA supplementation ameliorated albuminuria, bolstered the integrity of the glomerular filtration barrier, and mitigated mitochondrial impairments in GECs. Mechanistically, IPA hindered SIRT1 phosphorylation-mediated ubiquitin-proteasome degradation, restoring SIRT1's role in promoting PGC-1&#x3b1; deacetylation and nuclear translocation, thereby upregulating genes associated with mitochondrial biosynthesis and antioxidant defense.<br><br>CONCLUSION: Our findings underscore the potential of the microbial metabolite IPA to attenuate DKD progression, offering novel insights and potential therapeutic strategies for its management.},
}
@article {pmid39147055,
year = {2024},
author = {Lu, J and Qing, C and Huang, X and Zeng, J and Zheng, Y and Xia, P},
title = {Seasonal dynamics and driving mechanisms of microbial biogenic elements cycling function, assembly process, and co-occurrence network in plateau lake sediments.},
journal = {The Science of the total environment},
volume = {951},
number = {},
pages = {175510},
doi = {10.1016/j.scitotenv.2024.175510},
pmid = {39147055},
issn = {1879-1026},
mesh = {*Lakes/microbiology/chemistry ; *Geologic Sediments/microbiology ; *Seasons ; *Phosphorus/analysis ; *Microbiota ; *Nitrogen/analysis ; China ; Environmental Monitoring ; Bacteria/classification/genetics ; Carbon/analysis/metabolism ; },
abstract = {Microbial community diversity significantly varies with seasonality. However, little is known about seasonal variation of microbial community functions in lake sediments and their associated environmental influences. In this study, metagenomic sequencing of sediments collected from winter, summer, and autumn from Caohai Lake, Guizhou Plateau, were used to evaluate the composition and function of sediment microbial communities, the potential interactions of functional genes, key genes associated with seasons, and community assembly mechanisms. The average concentrations of nitrogen (TN) and phosphorus (TP) in lake sediments were higher, which were 6.136 and 0.501 g/kg, respectively. TN and organic matter (OM) were the primary factors associated with sediment community composition and functional profiles. The diversity and structure of the microbial communities varied with seasons, and Proteobacteria relative abundances were significantly lower in summer than in other seasons (58.43-44.12 %). Seasons were also associated with the relative abundances of functional genes, and in particular korA, metF, narC, nrfA, pstC/S, and soxB genes. Network complexity was highest in the summer and key genes in the network also varied across seasons. Neutral community model analysis revealed that the assembly mechanisms related to carbon (C), nitrogen (N), phosphorus (P), and sulfur (S) cycle-related genes were primarily associated with random processes. In summary, diverse functional genes were identified in lake sediments and exhibited evidence for synergistic interactions (Positive proportion: 74.91-99.82 %), while seasonal factors influenced their distribution. The results of this study provide new insights into seasonal impacts on microbial-driven biogeochemical cycling in shallow lakes.},
}
@article {pmid39146922,
year = {2024},
author = {Yuan, Y and Mo, C and Huang, F and Liao, X and Yang, Y},
title = {Microbial metabolism affects the antibiotic resistome in the intestine of laying hens.},
journal = {Poultry science},
volume = {103},
number = {10},
pages = {104138},
pmid = {39146922},
issn = {1525-3171},
mesh = {Animals ; *Chickens/microbiology ; *Gastrointestinal Microbiome/drug effects ; Female ; Anti-Bacterial Agents/pharmacology ; Escherichia coli/drug effects/genetics ; Drug Resistance, Microbial/genetics ; Drug Resistance, Bacterial ; Bacteria/drug effects/genetics/classification ; Intestines/microbiology/drug effects ; Cecum/microbiology ; },
abstract = {Intestinal microbial metabolism has an important impact on the health of laying hens, and microbes are also important hosts for ARGs. However, the relationship between intestinal microbes and antibiotic resistance in laying hens is unclear. In this study, a slaughtering experiment, an in vitro fermentation experiment and a single-bacteria culture experiment were carried out, and metagenomic and metabolomic analyses were used to investigate the relationships between microbial metabolism and the antibiotic resistome in the cecum of laying hens. The results showed that there were different types of ARGs in the intestines of laying hens, and the risk scores of the ARGs tended to decrease with growth stage. A total of 1142 metagenome-assembled genomes (MAGs) were obtained, and Escherichia coli was found to be the dominant ARG host, carrying 62 ARGs. Metabolomics revealed that indole and its derivatives, such as indole-3-lactic acid, were negatively correlated with a variety of ARGs. Moreover, in vitro fermentation experiment and single-bacteria culture experiment demonstrated that indole-3-lactic acid reduced the abundance and risk of multiple ARGs in the intestine and inhibited the growth of the ARG host Escherichia coli. In the context of high concern about intestinal microbial metabolism and antibiotic resistance, this is the first study to focus on the relationship between intestinal microbial metabolism and antibiotic resistance in laying hens. These findings have important implications for healthy farming and antibiotic resistance control.},
}
@article {pmid39146704,
year = {2024},
author = {Li, G and Wu, M and Xiao, Y and Tong, Y and Li, S and Qian, H and Zhao, T},
title = {Multi-omics reveals the ecological and biological functions of Enterococcus mundtii in the intestine of lepidopteran insects.},
journal = {Comparative biochemistry and physiology. Part D, Genomics &amp; proteomics},
volume = {52},
number = {},
pages = {101309},
doi = {10.1016/j.cbd.2024.101309},
pmid = {39146704},
issn = {1878-0407},
abstract = {Insect guts offer unique habitats for microbial colonization, with gut bacteria potentially offering numerous benefits to their hosts. Although Enterococcus has emerged as one of the predominant gut commensal bacteria in insects, its establishment in various niches within the gut has not been characterized well. In this study, Enterococcus mundtii was inoculated into the silkworm (Bombyx mori L.) to investigate its biological functions. Genome-based analysis revealed that its successful colonization is related to adherence genes (ebpA, ebpC, efaA, srtC, and scm). This bacterium did not alter the activities of related metabolic enzymes or the intestinal barrier function. However, significant changes in the gene expressions levels of Att2, CecA, and Lys suggest potential adaptive mechanisms of host immunity to symbiotic E. mundtii. Moreover, 16S metagenomics analysis revealed a significant increase in the relative abundance of E. mundtii in the intestines of silkworms following inoculation. The intestinal microbiome displayed marked heterogeneity, an elevated gut microbiome health index, a reduced microbial dysbiosis index, and low potential pathogenicity in the treatment group. Additionally, E. mundtii enhanced the breakdown of carbohydrates in host intestines. Overall, E. mundtii serves as a beneficial microbe for insects, promoting intestinal homeostasis by providing competitive advantage. This characteristic helps E. mundtii dominate complex microbial environments and remain prevalent across Lepidoptera, likely fostering long-term symbiosis between the both parties. The present study contributes to clarifying the niche of E. mundtii in the intestine of lepidopteran insects and further reveals its potential roles in their insect hosts.},
}
@article {pmid39146635,
year = {2024},
author = {Jang, TL and Scherger, SJ and Kalil, AC and Gomez, CA},
title = {Ehrlichiosis and anaplasmosis in solid organ transplantation: A case series and review of the literature.},
journal = {Diagnostic microbiology and infectious disease},
volume = {110},
number = {3},
pages = {116484},
doi = {10.1016/j.diagmicrobio.2024.116484},
pmid = {39146635},
issn = {1879-0070},
mesh = {Humans ; *Anaplasmosis/diagnosis/microbiology ; *Ehrlichiosis/diagnosis/drug therapy/microbiology ; Male ; Middle Aged ; Female ; *Organ Transplantation/adverse effects ; Adult ; Aged ; DNA, Bacterial/genetics ; Transplant Recipients ; },
abstract = {Ehrlichiosis and anaplasmosis are rising tickborne infections posing significant risks to solid-organ transplant (SOT) patients. We present three cases highlighting clinical presentations, diagnostic challenges, and the benefits of microbial cell-free DNA (mcfDNA) sequencing. Emphasizing early diagnosis and preventive measures, we advocate for advanced diagnostic modalities to improve outcomes in this vulnerable population.},
}
@article {pmid39145585,
year = {2024},
author = {Liu, B and Wang, G and Wang, L and Yan, J and Zhu, K and Liu, Q and Zhao, J and Jia, B and Fang, M and Rudich, Y and Morawska, L and Chen, J},
title = {Unraveling Cross-Organ Impacts of Airborne Pollutants: A Multiomics Study on Respiratory Exposure and Gastrointestinal Health.},
journal = {Environmental science &amp; technology},
volume = {58},
number = {35},
pages = {15511-15521},
doi = {10.1021/acs.est.4c06035},
pmid = {39145585},
issn = {1520-5851},
mesh = {Mice ; Animals ; *Air Pollutants/toxicity ; Inhalation Exposure ; Gastrointestinal Microbiome/drug effects ; Gastrointestinal Tract/drug effects ; Multiomics ; },
abstract = {Poor air quality is increasingly linked to gastrointestinal diseases, suggesting a potential correlation with human intestine health. However, this relationship remains largely unexplored due to limited research. This study used a controlled mouse model exposed to cooking oil fumes (COFs) and metagenomics, transcriptomics, and metabolomics to elucidate interactions between intestine microbiota and host metabolism under environmental stress. Our findings reveal that short-term COF inhalation induces pulmonary inflammation within 3 days and leads to gastrointestinal disturbances, elucidating a pathway connecting respiratory exposure to intestinal dysfunction. The exposure intensity significantly correlates with changes in intestinal tissue integrity, microbial composition, and metabolic function. Extended exposure of 7 days disrupts intestine microbiota and alters tryptophan metabolism, with further changes observed after 14 days, highlighting an adaptive response. These results highlight the vulnerability of intestinal health to airborne pollutants and suggest a pathway through which inhaled pollutants may affect distant organ systems.},
}
@article {pmid39145536,
year = {2024},
author = {Pipes, L and Nielsen, R},
title = {A rapid phylogeny-based method for accurate community profiling of large-scale metabarcoding datasets.},
journal = {eLife},
volume = {13},
number = {},
pages = {},
pmid = {39145536},
issn = {2050-084X},
support = {BIO180028//Pittsburgh Supercomputing Center/ ; 1R01GM138634-01/GM/NIGMS NIH HHS/United States ; 1K99GM144747-01/GM/NIGMS NIH HHS/United States ; BIO180028//Advanced Cyberinfrastructure Coordination Ecosystem: Services &amp; Support/ ; R01 GM138634/GM/NIGMS NIH HHS/United States ; K99 GM144747/GM/NIGMS NIH HHS/United States ; },
mesh = {*Phylogeny ; *DNA Barcoding, Taxonomic/methods ; Computational Biology/methods ; DNA, Environmental/genetics ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {Environmental DNA (eDNA) is becoming an increasingly important tool in diverse scientific fields from ecological biomonitoring to wastewater surveillance of viruses. The fundamental challenge in eDNA analyses has been the bioinformatical assignment of reads to taxonomic groups. It has long been known that full probabilistic methods for phylogenetic assignment are preferable, but unfortunately, such methods are computationally intensive and are typically inapplicable to modern next-generation sequencing data. We present a fast approximate likelihood method for phylogenetic assignment of DNA sequences. Applying the new method to several mock communities and simulated datasets, we show that it identifies more reads at both high and low taxonomic levels more accurately than other leading methods. The advantage of the method is particularly apparent in the presence of polymorphisms and/or sequencing errors and when the true species is not represented in the reference database.},
}
@article {pmid39144681,
year = {2024},
author = {Páez-Watson, T and Tomás-Martínez, S and de Wit, R and Keisham, S and Tateno, H and van Loosdrecht, MCM and Lin, Y},
title = {Sweet Secrets: Exploring Novel Glycans and Glycoconjugates in the Extracellular Polymeric Substances of "Candidatus Accumulibacter".},
journal = {ACS ES&amp;T water},
volume = {4},
number = {8},
pages = {3391-3399},
pmid = {39144681},
issn = {2690-0637},
abstract = {Biological wastewater treatment relies on microorganisms that grow as flocs, biofilms, or granules for efficient separation of biomass from cleaned water. This biofilm structure emerges from the interactions between microbes that produce, and are embedded in, extracellular polymeric substances (EPS). The true composition and structure of the EPS responsible for dense biofilm formation are still obscure. We conducted a bottom-up approach utilizing advanced glycomic techniques to explore the glycan diversity in the EPS from a highly enriched "Candidatus Accumulibacter" granular sludge. Rare novel sugar monomers such as N-Acetylquinovosamine (QuiNAc) and 2-O-Methylrhamnose (2-OMe-Rha) were identified to be present in the EPS of both enrichments. Further, a high diversity in the glycoprotein structures of said EPS was identified by means of lectin based microarrays. We explored the genetic potential of "Ca. Accumulibacter" high quality metagenome assembled genomes (MAGs) to showcase the shortcoming of top-down bioinformatics based approaches at predicting EPS composition and structure, especially when dealing with glycans and glycoconjugates. This work suggests that more bottom-up research is necessary to understand the composition and complex structure of EPS in biofilms since genome based inference cannot directly predict glycan structures and glycoconjugate diversity.},
}
@article {pmid39144493,
year = {2024},
author = {Geraldi, NR and Acinas, SG and Alam, I and Gasol, JM and Fernández-de-Puelles, ML and Giner, CR and Hernández León, S and Logares, R and Massana, R and Sánchez, P and Bajic, V and Gojobori, T and Duarte, CM},
title = {Assessing patterns of metazoans in the global ocean using environmental DNA.},
journal = {Royal Society open science},
volume = {11},
number = {8},
pages = {240724},
pmid = {39144493},
issn = {2054-5703},
abstract = {Documenting large-scale patterns of animals in the ocean and determining the drivers of these patterns is needed for conservation efforts given the unprecedented rates of change occurring within marine ecosystems. We used existing datasets from two global expeditions, Tara Oceans and Malaspina, that circumnavigated the oceans and sampled down to 4000 m to assess metazoans from environmental DNA (eDNA) extracted from seawater. We describe patterns of taxonomic richness within metazoan phyla and orders based on metabarcoding and infer the relative abundance of phyla using metagenome datasets, and relate these data to environmental variables. Arthropods had the greatest taxonomic richness of metazoan phyla at the surface, while cnidarians had the greatest richness in pelagic zones. Half of the marine metazoan eDNA from metagenome datasets was from arthropods, followed by cnidarians and nematodes. We found that mean surface temperature and primary productivity were positively related to metazoan taxonomic richness. Our findings concur with existing knowledge that temperature and primary productivity are important drivers of taxonomic richness for specific taxa at the ocean's surface, but these correlations are less evident in the deep ocean. Massive sequencing of eDNA can improve understanding of animal distributions, particularly for the deep ocean where sampling is challenging.},
}
@article {pmid39144222,
year = {2024},
author = {Li, Y and Liu, M and Kong, B and Zhang, G and Zhang, Q},
title = {The role of selenium intervention in gut microbiota homeostasis and gene function in mice with breast cancer on a high-fat diet.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1439652},
pmid = {39144222},
issn = {1664-302X},
abstract = {OBJECTIVE: This study aimed to investigate the effect of selenium on gut microbiota in mice with breast cancer under a high-fat diet.<br><br>METHODS: A total of 12 female BALB/c mice were randomly divided into two groups: 4&#x2009;T1&#x2009;+&#x2009;selenium+ high-fat diet group and 4&#x2009;T1&#x2009;+&#x2009;high-fat diet group. Mice were injected with 4&#x2009;T1 cells on the right 4th mammary fat pad and kept on a high-fat diet. Fecal samples were collected, and DNA was extracted for metagenomic sequencing and bioinformatics analysis. Relevant target genes and pathways were annotated and metabolically analyzed to explore the intervention effect of selenium on breast cancer in the high-fat diet state.<br><br>RESULTS: Selenium supplementation in the high-fat diet altered the composition and diversity of gut microbiota in mice with breast cancer. The gut microbial composition was significantly different in the selenium intervention group, with an increased abundance of Proteobacteria, Actinobacteria, and Verrucomicrobia phyla and species such as Helicobacter ganmani, Helicobacter japonicus, and Akkermansia muciniphila, while phyla, such as Bacteroidetes, Firmicutes, Deferribacteres, and Spirochaetes, and species, such as Prevotella sp. MGM2, Muribaculum intestinale, Lactobacillus murinus, and Prevotella sp. MGM1, were decreased. Functional analysis revealed differential expression of genes related to carbohydrate-active enzymes, pathogen-host interactions, cell communication, cell auto-induction, membrane transporters, and virulence factors. Furthermore, 37 COGs and 48 metabolites with rising metabolic potential in the selenium intervention group were predicted.<br><br>CONCLUSION: Selenium alters the homeostasis of gut microbiota in mice with breast cancer on a high-fat diet, affecting their composition, abundance, and associated metabolism. These findings suggest that the mechanism involves interfering with gut microbiota homeostasis, leading to altered synthesis of tumor-associated proteins and fatty acids and inducing tumor cell apoptosis and pyroptosis.},
}
@article {pmid39144212,
year = {2024},
author = {Gtari, M and Maaoui, R and Ghodhbane-Gtari, F and Ben Slama, K and Sbissi, I},
title = {MAGs-centric crack: how long will, spore-positive Frankia and most Protofrankia, microsymbionts remain recalcitrant to axenic growth?.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1367490},
pmid = {39144212},
issn = {1664-302X},
abstract = {Nearly 50 years after the ground-breaking isolation of the primary Comptonia peregrina microsymbiont under axenic conditions, efforts to isolate a substantial number of Protofrankia and Frankia strains continue with enduring challenges and complexities. This study aimed to streamline genomic insights through comparative and predictive tools to extract traits crucial for isolating specific Frankia in axenic conditions. Pangenome analysis unveiled significant genetic diversity, suggesting untapped potential for cultivation strategies. Shared metabolic strategies in cellular components, central metabolic pathways, and resource acquisition traits offered promising avenues for cultivation. Ecological trait extraction indicated that most uncultured strains exhibit no apparent barriers to axenic growth. Despite ongoing challenges, potential caveats, and errors that could bias predictive analyses, this study provides a nuanced perspective. It highlights potential breakthroughs and guides refined cultivation strategies for these yet-uncultured strains. We advocate for tailored media formulations enriched with simple carbon sources in aerobic environments, with atmospheric nitrogen optionally sufficient to minimize contamination risks. Temperature adjustments should align with strain preferences-28-29°C for Frankia and 32-35°C for Protofrankia-while maintaining an alkaline pH. Given potential extended incubation periods (predicted doubling times ranging from 3.26 to 9.60 days, possibly up to 21.98 days), patience and rigorous contamination monitoring are crucial for optimizing cultivation conditions.},
}
@article {pmid39143609,
year = {2024},
author = {Shaw, J and Yu, YW},
title = {Fairy: fast approximate coverage for multi-sample metagenomic binning.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {151},
pmid = {39143609},
issn = {2049-2618},
support = {CGS-D//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN-2022-309 03074//Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {*Metagenomics/methods ; *Metagenome ; Software ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; Archaea/genetics/classification ; Algorithms ; },
abstract = {BACKGROUND: Metagenomic binning, the clustering of assembled contigs that belong to the same genome, is a crucial step for recovering metagenome-assembled genomes (MAGs). Contigs are linked by exploiting consistent signatures along a genome, such as read coverage patterns. Using coverage from multiple samples leads to higher-quality MAGs; however, standard pipelines require all-to-all read alignments for multiple samples to compute coverage, becoming a key computational bottleneck.<br><br>RESULTS: We present fairy (https://github.com/bluenote-1577/fairy), an approximate coverage calculation method for metagenomic binning. Fairy is a fast k-mer-based alignment-free method. For multi-sample binning, fairy can be > 250 &#xd7; faster than read alignment and accurate enough for binning. Fairy is compatible with several existing binners on host and non-host-associated datasets. Using MetaBAT2, fairy recovers 98.5 % of MAGs with > 50 % completeness and < 5 % contamination relative to alignment with BWA. Notably, multi-sample binning with fairy is always better than single-sample binning using BWA (> 1.5 &#xd7; more > 50 % complete MAGs on average) while still being faster. For a public sediment metagenome project, we demonstrate that multi-sample binning recovers higher quality Asgard archaea MAGs than single-sample binning and that fairy's results are indistinguishable from read alignment.<br><br>CONCLUSIONS: Fairy is a new tool for approximately and quickly calculating multi-sample coverage for binning, resolving a computational bottleneck for metagenomics. Video Abstract.},
}
@article {pmid39143554,
year = {2024},
author = {Francis, D and Sun, F},
title = {A comparative analysis of mutual information methods for pairwise relationship detection in metagenomic data.},
journal = {BMC bioinformatics},
volume = {25},
number = {1},
pages = {266},
pmid = {39143554},
issn = {1471-2105},
support = {EF-2125142//National Science Foundation/ ; EF-2125142//National Science Foundation/ ; },
mesh = {*Metagenomics/methods ; Algorithms ; Metagenome/genetics ; },
abstract = {BACKGROUND: Construction of co-occurrence networks in metagenomic data often employs correlation to infer pairwise relationships between microbes. However, biological systems are complex and often display qualities non-linear in nature. Therefore, the reliance on correlation alone may overlook important relationships and fail to capture the full breadth of intricacies presented in underlying interaction networks. It is of interest to incorporate metrics that are not only robust in detecting linear relationships, but non-linear ones as well.<br><br>RESULTS: In this paper, we explore the use of various mutual information (MI) estimation approaches for quantifying pairwise relationships in biological data and compare their performances against two traditional measures-Pearson's correlation coefficient, r, and Spearman's rank correlation coefficient, &#x3c1;. Metrics are tested on both simulated data designed to mimic pairwise relationships that may be found in ecological systems and real data from a previous study on C. diff infection. The results demonstrate that, in the case of asymmetric relationships, mutual information estimators can provide better detection ability than Pearson's or Spearman's correlation coefficients. Specifically, we find that these estimators have elevated performances in the detection of exploitative relationships, demonstrating the potential benefit of including them in future metagenomic studies.<br><br>CONCLUSIONS: Mutual information (MI) can uncover complex pairwise relationships in biological data that may be missed by traditional measures of association. The inclusion of such relationships when constructing co-occurrence networks can result in a more comprehensive analysis than the use of correlation alone.},
}
@article {pmid39143383,
year = {2024},
author = {Vijayan, J and Ezhuthanikkunnel, AP and Punnorkodu, SAK and Poikayil, SS and Mohan, M and Ammanamveetil, MHA},
title = {Sediment microbial diversity, functional potentials, and antibiotic resistance pattern: a case study of Cochin Estuary core sediment.},
journal = {Environmental science and pollution research international},
volume = {31},
number = {39},
pages = {52132-52146},
pmid = {39143383},
issn = {1614-7499},
mesh = {*Geologic Sediments/microbiology ; *Estuaries ; India ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Phylogeny ; Biodiversity ; },
abstract = {Marine sediments are an important part of the marine environment and the world's greatest organic carbon source. Sediment microorganisms are important regulators of major geochemical and eco-environmental processes in marine environments, especially nutrient dynamics and biogeochemical cycles. Despite their importance, core marine microorganisms are virtually unknown due to a lack of consensus on how to identify them. Most core microbiotas have been characterized thus far based on species abundance and occurrence. The combined effects of habitat and depth on benthic bacterial communities and ecological functions were studied using "Next-Generation sequencing (NGS) and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) predictive functional profiling" at the surface (0.2 cm) and bottom depth (250 cm) in a sediment core sample from Cochin Estuary, Kerala, India. The results showed that bacterial diversity and richness were significantly higher in the surface sediment sample with the most abundant phyla being Proteobacteria, Acidobacteria, Chloroflexi, and Bacteroidetes. The major metabolic functions were metabolism, followed by environmental information processing and genetic information processing. Antibiotic resistance genes between the surface and bottom samples help to understand the resistance pattern among multidrug resistance is the most prominent one. Among viruses, Siphoviridae is the dominant family, followed by Myoviridae. In the case of Archea, Crenarchaeota is dominant, whereas among eukaryotes phyla Streptophyta and Chordata were dominant in the surface and the bottom samples respectively.},
}
@article {pmid39143364,
year = {2024},
author = {Akhlaghi, E and Salari, E and Mansouri, M and Shafiei, M and Kalantar-Neyestanaki, D and Aghassi, H and Fasihi Harandi, M},
title = {Identification and comparison of intestinal microbial diversity in patients at different stages of hepatic cystic echinococcosis.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {18912},
pmid = {39143364},
issn = {2045-2322},
support = {400000473//Kerman University of Medical Sciences/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Echinococcosis, Hepatic/microbiology/parasitology ; Male ; Female ; *RNA, Ribosomal, 16S/genetics ; Adult ; Middle Aged ; Feces/microbiology/parasitology ; Bacteria/classification/genetics/isolation &amp; purification ; Biodiversity ; High-Throughput Nucleotide Sequencing ; },
abstract = {There is a significant focus on the role of the host microbiome in different outcomes of human parasitic diseases, including cystic echinococcosis (CE). This study was conducted to identify the intestinal microbiome of patients with CE at different stages of hydatid cyst compared to healthy individuals. Stool samples from CE patients as well as healthy individuals were collected. The samples were divided into three groups representing various stages of hepatic hydatid cyst: active (CE1 and CE2), transitional (CE3), and inactive (CE4 and CE5). One family member from each group was selected to serve as a control. The gut microbiome of patients with different stages of hydatid cysts was investigated using metagenomic next-generation amplicon sequencing of the V3-V4 region of the 16S rRNA gene. In this study, we identified 4862 Operational Taxonomic Units from three stages of hydatid cysts in CE patients and healthy individuals with a combined frequency of 2,955,291. The most abundant genera observed in all the subjects were Blautia, Agathobacter, Faecalibacterium, Bacteroides, Bifidobacterium, and Prevotella. The highest microbial frequency was related to inactive forms of CE, and the lowest frequency was observed in the group with active forms. However, the lowest OTU diversity was found in patients with inactive cysts compared with those with active and transitional cyst stages. The genus Agatobacter had the highest OTU frequency. Pseudomonas, Gemella, and Ligilactobacillus showed significant differences among the patients with different stages of hydatid cysts. Additionally, Anaerostipes and Candidatus showed significantly different reads in CE patients compared to healthy individuals. Our findings indicate that several bacterial genera can play a role in the fate of hydatid cysts in patients at different stages of the disease.},
}
@article {pmid39143178,
year = {2024},
author = {Duru, IC and Lecomte, A and Shishido, TK and Laine, P and Suppula, J and Paulin, L and Scheperjans, F and Pereira, PAB and Auvinen, P},
title = {Metagenome-assembled microbial genomes from Parkinson's disease fecal samples.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {18906},
pmid = {39143178},
issn = {2045-2322},
support = {NNF22OC0080109//Novo Nordisk Foundation/ ; },
mesh = {*Parkinson Disease/genetics/microbiology ; Humans ; *Feces/microbiology ; *Metagenome ; *Gastrointestinal Microbiome/genetics ; Metagenomics/methods ; Genome, Bacterial ; Male ; Aged ; Female ; Genome, Microbial ; Middle Aged ; High-Throughput Nucleotide Sequencing ; },
abstract = {The human gut microbiome composition has been linked to Parkinson's disease (PD). However, knowledge of the gut microbiota on the genome level is still limited. Here we performed deep metagenomic sequencing and binning to build metagenome-assembled genomes (MAGs) from 136 human fecal microbiomes (68 PD samples and 68 control samples). We constructed 952 non-redundant high-quality MAGs and compared them between PD and control groups. Among these MAGs, there were 22 different genomes of Collinsella and Prevotella, indicating high variability of those genera in the human gut environment. Microdiversity analysis indicated that Ruminococcus bromii was statistically significantly (p < 0.002) more diverse on the strain level in the control samples compared to the PD samples. In addition, by clustering all genes and performing presence-absence analysis between groups, we identified several control-specific (p < 0.05) related genes, such as speF and Fe-S oxidoreductase. We also report detailed annotation of MAGs, including Clusters of Orthologous Genes (COG), Cas operon type, antiviral gene, prophage, and secondary metabolites biosynthetic gene clusters, which can be useful for providing a reference for future studies.},
}
@article {pmid39143108,
year = {2024},
author = {Grahnemo, L and Kambur, O and Lahti, L and Jousilahti, P and Niiranen, T and Knight, R and Salomaa, V and Havulinna, AS and Ohlsson, C},
title = {Associations between gut microbiota and incident fractures in the FINRISK cohort.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {69},
pmid = {39143108},
issn = {2055-5008},
support = {NNF 190C0055250 and 22OC0078421//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; 101096347/ERC_/European Research Council/International ; KAW 2015.0317//Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation)/ ; LU2021-0096//IngaBritt och Arne Lundbergs Forskningsstiftelse (Ingabritt and Arne Lundberg Research Foundation)/ ; 2020-01392//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; },
mesh = {*Gastrointestinal Microbiome ; Humans ; Male ; Female ; *Fractures, Bone/microbiology/epidemiology/etiology ; Middle Aged ; Finland/epidemiology ; Aged ; Bacteria/classification/genetics/isolation &amp; purification ; Metagenome ; Cohort Studies ; Incidence ; Metagenomics/methods ; Proteobacteria/genetics/isolation &amp; purification ; Risk Factors ; Adult ; },
abstract = {The gut microbiota (GM) can regulate bone mass, but its association with incident fractures is unknown. We used Cox regression models to determine whether the GM composition is associated with incident fractures in the large FINRISK 2002 cohort (n = 7043, 1092 incident fracture cases, median follow-up time 18 years) with information on GM composition and functionality from shotgun metagenome sequencing. Higher alpha diversity was associated with decreased fracture risk (hazard ratio [HR] 0.92 per standard deviation increase in Shannon index, 95% confidence interval 0.87-0.96). For beta diversity, the first principal component was associated with fracture risk (Aitchison distance, HR 0.90, 0.85-0.96). In predefined phyla analyses, we observed that the relative abundance of Proteobacteria was associated with increased fracture risk (HR 1.14, 1.07-1.20), while the relative abundance of Tenericutes was associated with decreased fracture risk (HR 0.90, 0.85-0.96). Explorative sub-analyses within the Proteobacteria phylum showed that higher relative abundance of Gammaproteobacteria was associated with increased fracture risk. Functionality analyses showed that pathways related to amino acid metabolism and lipopolysaccharide biosynthesis associated with fracture risk. The relative abundance of Proteobacteria correlated with pathways for amino acid metabolism, while the relative abundance of Tenericutes correlated with pathways for butyrate synthesis. In conclusion, the overall GM composition was associated with incident fractures. The relative abundance of Proteobacteria, especially Gammaproteobacteria, was associated with increased fracture risk, while the relative abundance of Tenericutes was associated with decreased fracture risk. Functionality analyses demonstrated that pathways known to regulate bone health may underlie these associations.},
}
@article {pmid39143045,
year = {2024},
author = {Baldi, A and Braat, S and Imrul Hasan, M and Bennett, C and Barrios, M and Jones, N and Moir-Meyer, G and Abdul Azeez, I and Wilcox, S and Saiful Alam Bhuiyan, M and Ataide, R and Clucas, D and Harrison, LC and Arifeen, SE and Bowden, R and Biggs, BA and Jex, A and Pasricha, SR},
title = {Community use of oral antibiotics transiently reprofiles the intestinal microbiome in young Bangladeshi children.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {6980},
pmid = {39143045},
issn = {2041-1723},
support = {GNT1103262//Department of Health | National Health and Medical Research Council (NHMRC)/ ; GNT1158696//Department of Health | National Health and Medical Research Council (NHMRC)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/genetics ; Bangladesh/epidemiology ; Infant ; *Anti-Bacterial Agents/administration &amp; dosage/pharmacology ; *RNA, Ribosomal, 16S/genetics ; Male ; Female ; Administration, Oral ; Drug Resistance, Bacterial/genetics ; Feces/microbiology ; Metagenomics/methods ; Bacteria/genetics/drug effects/classification/isolation &amp; purification ; Cephalosporins/administration &amp; dosage/pharmacology/therapeutic use ; Enterococcus/drug effects/genetics/isolation &amp; purification ; Antimicrobial Stewardship ; },
abstract = {Antibiotics may alter the gut microbiome, and this is one of the mechanisms by which antimicrobial resistance may be promoted. Suboptimal antimicrobial stewardship in Asia has been linked to antimicrobial resistance. We aim to examine the relationship between oral antibiotic use and composition and antimicrobial resistance in the gut microbiome in 1093 Bangladeshi infants. We leverage a trial of 8-month-old infants in rural Bangladesh: 61% of children were cumulatively exposed to antibiotics (most commonly cephalosporins and macrolides) over the 12-month study period, including 47% in the first 3 months of the study, usually for fever or respiratory infection. 16S rRNA amplicon sequencing in 11-month-old infants reveals that alpha diversity of the intestinal microbiome is reduced in children who received antibiotics within the previous 7 days; these samples also exhibit enrichment for Enterococcus and Escherichia/Shigella genera. No effect is seen in children who received antibiotics earlier. Using shotgun metagenomics, overall abundance of antimicrobial resistance genes declines over time. Enrichment for an Enterococcus-related antimicrobial resistance gene is observed in children receiving antibiotics within the previous 7 days, but not earlier. Presence of antimicrobial resistance genes is correlated to microbiome composition. In Bangladeshi children, community use of antibiotics transiently reprofiles the gut microbiome.},
}
@article {pmid39142773,
year = {2024},
author = {Zaytsev, V and Tutukina, MN and Chetyrkina, MR and Shelyakin, PV and Ovchinnikov, G and Satybaldina, D and Kondrashov, VA and Bandurist, MS and Seilov, S and Gorin, DA and Fedorov, FS and Gelfand, MS and Nasibulin, AG},
title = {Monitoring of meat quality and change-point detection by a sensor array and profiling of bacterial communities.},
journal = {Analytica chimica acta},
volume = {1320},
number = {},
pages = {343022},
doi = {10.1016/j.aca.2024.343022},
pmid = {39142773},
issn = {1873-4324},
mesh = {*Electronic Nose ; *Bacteria/isolation &amp; purification ; Meat/microbiology/analysis ; Microbiota ; Animals ; Food Quality ; Food Microbiology ; },
abstract = {BACKGROUND: Real-time monitoring of food consumer quality remains challenging due to diverse bio-chemical processes taking place in the food matrices, and hence it requires accurate analytical methods. Thresholds to determine spoiled food are often difficult to set. The existing analytical methods are too complicated for rapid in situ screening of foodstuff.<br><br>RESULTS: We have studied the dynamics of meat spoilage by electronic nose (e-nose) for digitizing the smell associated with volatile spoilage markers of meat, comparing the results with changes in the microbiome composition of the spoiling meat samples. We apply the time series analysis to follow dynamic changes in the gas profile extracted from the e-nose responses and to identify the change-point window of the meat state. The obtained e-nose features correlate with changes in the microbiome composition such as increase in the proportion of Brochothrix and Pseudomonas spp. and disappearance of Mycoplasma spp., and with representative gas sensors towards hydrogen, ammonia, and alcohol vapors with R[2] values of 0.98, 0.93, and 0.91, respectively. Integration of e-nose and computer vision into a single analytical panel improved the meat state identification accuracy up to 0.85, allowing for more reliable meat state assessment.<br><br>SIGNIFICANCE: Accurate identification of the change-point in the meat state achieved by digitalizing volatile spoilage markers from the e-nose unit holds promises for application of smart miniaturized devices in food industry.},
}
@article {pmid39142657,
year = {2024},
author = {Hu, H and Ding, H and Lyu, J and Chen, Y and Huang, C and Zhang, C and Li, W and Fang, X and Zhang, W},
title = {Detection of rare microorganisms in bone and joint infections by metagenomic next-generation sequencing.},
journal = {Bone &amp; joint research},
volume = {13},
number = {8},
pages = {401-410},
pmid = {39142657},
issn = {2046-3758},
support = {//Natural Science Foundation of Fujian Province/ ; //Joint Funds for the Innovation of Science and Technology, Fujian province/ ; //Fujian Orthopaedic Bone and Joint Disease and Sports Rehabilitation Clinical Medical Research Center/ ; //Foreign Cooperation Project of Science and Technology, Fujian province/ ; },
abstract = {AIMS: This aim of this study was to analyze the detection rate of rare pathogens in bone and joint infections (BJIs) using metagenomic next-generation sequencing (mNGS), and the impact of mNGS on clinical diagnosis and treatment.<br><br>METHODS: A retrospective analysis was conducted on 235 patients with BJIs who were treated at our hospital between January 2015 and December 2021. Patients were divided into the no-mNGS group (microbial culture only) and the mNGS group (mNGS testing and microbial culture) based on whether mNGS testing was used or not.<br><br>RESULTS: A total of 147 patients were included in the no-mNGS group and 88 in the mNGS group. The mNGS group had a higher detection rate of rare pathogens than the no-mNGS group (21.6% vs 10.2%, p = 0.016). However, the mNGS group had lower rates of antibiotic-related complications, shorter hospital stays, and higher infection control rates compared with the no-mNGS group (p = 0.017, p = 0.003, and p = 0.028, respectively), while there was no significant difference in the duration of antibiotic use (p = 0.957). In culture-negative cases, the mNGS group had lower rates of antibiotic-related complications, shorter hospital stays, and a higher infection control rate than the no-mNGS group (p = 0.036, p = 0.033, p = 0.022, respectively), while there was no significant difference in the duration of antibiotic use (p = 0.748).<br><br>CONCLUSION: mNGS improves detection of rare pathogens in BJIs. mNGS testing reduces antibiotic-related complications, shortens hospital stay and antibiotic use duration, and improves treatment success rate, benefits which are particularly evident in culture-negative cases.},
}
@article {pmid39142630,
year = {2024},
author = {Li, Y and Qu, P and Ye, Y and Chen, L},
title = {Strongyloides stercoralis hyperinfection syndrome in immunocompetent patients.},
journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cmi.2024.08.008},
pmid = {39142630},
issn = {1469-0691},
}
@article {pmid39142392,
year = {2024},
author = {Carpenter, L and Miller, S and Flynn, E and Choo, JM and Collins, J and Shoubridge, AP and Gordon, D and Lynn, DJ and Whitehead, C and Leong, LEX and Ivey, KL and Wesselingh, SL and Inacio, MC and Crotty, M and Papanicolas, LE and Taylor, SL and Rogers, GB},
title = {Exposure to doxycycline increases risk of carrying a broad range of enteric antimicrobial resistance determinants in an elderly cohort.},
journal = {The Journal of infection},
volume = {89},
number = {4},
pages = {106243},
doi = {10.1016/j.jinf.2024.106243},
pmid = {39142392},
issn = {1532-2742},
mesh = {Humans ; Female ; Male ; Aged, 80 and over ; *Doxycycline/therapeutic use/pharmacology ; *Anti-Bacterial Agents/pharmacology ; Cross-Sectional Studies ; *Feces/microbiology ; Drug Resistance, Bacterial/genetics ; Cohort Studies ; South Australia/epidemiology ; Aged ; Metagenomics ; Carrier State/microbiology/epidemiology ; },
abstract = {OBJECTIVES: High rates of antibiotic prescription in residential aged care are likely to promote enteric carriage of antibiotic-resistant pathogens and increase the risk of antibiotic treatment failure. Despite their importance, relationships between antibiotic exposures and patterns of enteric resistance carriage in this population remain poorly understood.<br><br>METHODS: We conducted a cross-sectional metagenomic cohort analysis of stool samples from residents of five long-term aged-care facilities in South Australia. Taxonomic composition was determined, and enteric carriage of antibiotic resistance genes (ARGs) was identified and quantified against the Comprehensive Antibiotic Resistance Database. Both the detection and abundance of stool taxa and ARGs were related to antibiotic exposures up to 12 months prior. Factors associated with the abundance of ARGs of high clinical concern were identified.<br><br>RESULTS: Stool samples were provided by 164 participants (median age: 88 years, IQR 81-93; 72% female). Sixty-one percent (n&#xa0;=&#xa0;100) of participants were prescribed antibiotics at least once in the prior 12 months (median prescriptions: 4, range: 1-52), most commonly a penicillin (n&#xa0;=&#xa0;55, 33.5%), cephalosporin (n&#xa0;=&#xa0;53, 32.3%), diaminopyrimidine (trimethoprim) (n&#xa0;=&#xa0;36, 22%), or tetracycline (doxycycline) (n&#xa0;=&#xa0;21, 12.8%). More than 1100 unique ARGs, conferring resistance to 38 antibiotic classes, were identified, including 20 ARGs of high clinical concern. Multivariate logistic regression showed doxycycline exposure to be the greatest risk factor for high ARG abundance (adjusted odds ratio [aOR]=14.8, q<0.001) and a significant contributor to inter-class selection, particularly for ARGs relating to penicillins (aOR=3.1, q=0.0004) and cephalosporins (aOR=3.4, q=0.003). High enteric ARG abundance was associated with the number of separate antibiotic exposures (aOR: 6.4, q<0.001), exposures within the prior 30 days (aOR: 4.6, q=0.008) and prior 30-100 days (aOR: 2.6, q=0.008), high duration of antibiotic exposure (aOR: 7.9, q<0.001), and exposure to 3 or more antibiotic classes (aOR: 7.4, q<0.001). Carriage of one or more ARGs of high clinical concern was identified in 99% of participants (n&#xa0;=&#xa0;162, median: 3, IQR: 2-4), involving 11 ARGs conferring resistance to aminoglycosides, four to beta-lactams, one to glycopeptides, three to fluoroquinolones, and one to oxazolidinones. Carriage of ARGs of high clinical concern was positively associated with exposure to doxycycline (aminoglycoside, fluoroquinolone, and oxazolidinone ARGs) and trimethoprim (fluoroquinolone and beta-lactam ARGs). Analysis of doxycycline impact on microbiota composition suggested that observed resistome changes arose principally through direct ARG selection, rather than through the antibiotic depletion of sensitive bacterial populations.<br><br>CONCLUSIONS: The gut microbiome of aged care residents is a major reservoir of antibiotic resistance. As a critical antibiotic in medical practice, a comprehensive understanding of the impact of doxycycline exposure on the gut resistome is paramount for informed antibiotic use, particularly in an evolving landscape of prophylactic applications. Near-universal asymptomatic carriage of clinically critical resistance determinants is highly concerning and reinforces the urgent need for improved management of antibiotic use in long-term aged care.},
}
@article {pmid39142045,
year = {2024},
author = {Xu, D and Pan, C and Liu, S and Guo, J and Zheng, P and Zhang, M},
title = {Efficient alleviation granular sludge floatation in a high-rate anammox reactor by dosing folate.},
journal = {Water research},
volume = {264},
number = {},
pages = {122249},
doi = {10.1016/j.watres.2024.122249},
pmid = {39142045},
issn = {1879-2448},
mesh = {*Sewage/microbiology ; *Bioreactors ; *Folic Acid/metabolism ; Waste Disposal, Fluid/methods ; Nitrogen/metabolism ; Bacteria/metabolism ; Anaerobiosis ; },
abstract = {Although granular floatation has been recognized as a significant issue hindering the application of high-rate anammox biotechnology, limited knowledge is available about its causes and control strategies. This study proposed a novel control strategy by adding folate, and demonstrated its role in the granular floatation alleviation through long-term operation and granular characterizations. It was found that the floatation of anammox granular sludge was obviously relieved with the decreased sludge floatation potential by 67.1% after dosing with folate (8 mg/L) at a high nitrogen loading rate of 12.3 kg-N/(m[3]·d). Physiochemical analyses showed that the decrease of extracellular polymeric substances (EPS) content (mainly protein), the alleviation of granular surface pore plugging in conjunction with the smooth discharge of generated nitrogen gas were collectively responsible for efficient floatation control. Moreover, metagenomic analysis suggested that the synergistic interactions between anammox bacteria and their symbionts were attenuated after dosing exogenous folate. Anammox bacteria would reduce their synergistic dependence on the symbionts, and decline the supply of metabolites (e.g., amino acids and carbohydrates in EPS) to symbiotic bacteria. The declined EPS excretion contributed to the alleviation of granular floatation by dredging pores blockage, thus leading to a stable system performance. The findings not only offer insights into the role of microbial interaction in granular sludge floatation, but also provide a feasible approach for controlling the floatation issue in anammox granular-based processes.},
}
@article {pmid39141834,
year = {2024},
author = {Xu, Y and Leung, SKK and Li, TMW and Yung, CCM},
title = {Hidden genomic diversity drives niche partitioning in a cosmopolitan eukaryotic picophytoplankton.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {39141834},
issn = {1751-7370},
support = {26100521//Research Grants Council of Hong Kong/ ; },
mesh = {*Phytoplankton/genetics/classification ; *Phylogeny ; *Genetic Variation ; Metagenomics ; Genomics ; Temperature ; Ecosystem ; },
abstract = {Marine eukaryotic phytoplankton are fundamental to the marine food web, yet the lack of reference genomes or just a single genome representing a taxon has led to an underestimation of their taxonomic, adaptive, and functional diversity. Here, we integrated strain isolation with metagenomic binning to recover genomes from the cosmopolitan picophytoplankton genus Bathycoccus, traditionally considered monospecific. Our recovery and analysis of 37 Bathycoccus genomes delineated their global genomic diversity and established four evolutionary clades (BI, BII, BIII, BIV). Our metagenomic abundance survey revealed well-differentiated ecological niches and distinct biogeographic distributions for each clade, predominantly shaped by temperature, salinity, and nutrient availability. Comparative genomics analyses further revealed clade-specific genomic traits that underpin niche adaptation and contribute to the global prevalence of Bathycoccus. Our findings underscore temperature as a major driver of genome diversification in this genus, with clade divergences coinciding with major paleoclimatic events that influenced their contemporary thermal niches. Moreover, the unique enrichment of C2H2 zinc finger and ankyrin repeat gene families in polar-adapted clades suggests previously unrecognized cold-adaptation mechanisms in marine eukaryotic phytoplankton. Our study offers a comprehensive genomic landscape of this crucial eukaryotic picophytoplankton, providing insights into their microdiversity and adaptive evolution in response to changing environments.},
}
@article {pmid39141752,
year = {2024},
author = {Gu, J and Lei, B and Wang, Z and Zhang, T and Jiang, T and Zhang, P and Chen, W and Zhang, Y and Jiang, R and Xu, G and Chang, Q and Zhou, M},
title = {Dynamic Viral Load Monitoring and Metagenomic Sequencing in Acute Retinal Necrosis Caused by Varicella-Zoster Virus.},
journal = {Retina (Philadelphia, Pa.)},
volume = {},
number = {},
pages = {},
doi = {10.1097/IAE.0000000000004214},
pmid = {39141752},
issn = {1539-2864},
abstract = {PURPOSE: To analyze the trend of intraocular viral load after antiviral treatment in patients with varicella-zoster virus (VZV) induced acute retinal necrosis (ARN), and to explore the effect of viral genotypes on clinical manifestations.<br><br>METHODS: In this case series, viral load was detected using polymerase chain reaction from aqueous humor during treatment; viral load curves were fitted, and the time required to reach the inflection point between plateau phase and logarithmic reduction phase (Tinflection) was estimated. Variations in viral genomes were detected by metagenomic sequencing.<br><br>RESULTS: Twenty eyes of 20 patients were included. The median (interquartile range) initial viral load was 5.9&#xd7;107 (1.1&#xd7;107-1.1&#xd7;108) copies/mL. The average duration of retinitis was 5&#xb1;3 weeks. The average Tinflection was 4.2&#xb1;1.6 days. Tinflection was correlated with the duration of retinitis (P=0.025). Patients with VZVs carrying the p.S715* variation in ribonucleotide reductase (RNR) subunit 1 gene had lower initial viral loads (median 1.3&#xd7;107 copies/ml) than those without (median 1.1&#xd7;108 copies/ml; adjusted P=0.030).<br><br>CONCLUSIONS: The inflection of viral load curve is helpful to estimate the length of plateau phase and the duration of retinitis during antiviral treatment in ARN patients. Loss-of-function variation in RNR gene might be correlated with lower virulence of VZV.},
}
@article {pmid39141729,
year = {2024},
author = {Lai, S and Wang, H and Bork, P and Chen, WH and Zhao, XM},
title = {Long-read sequencing reveals extensive gut phageome structural variations driven by genetic exchange with bacterial hosts.},
journal = {Science advances},
volume = {10},
number = {33},
pages = {eadn3316},
pmid = {39141729},
issn = {2375-2548},
mesh = {*Bacteriophages/genetics ; Humans ; *Gastrointestinal Microbiome/genetics ; *Bacteria/virology/genetics ; *Gene Transfer, Horizontal ; Metagenomics/methods ; Genetic Variation ; Virome/genetics ; Genome, Viral ; High-Throughput Nucleotide Sequencing ; },
abstract = {Genetic variations are instrumental for unraveling phage evolution and deciphering their functional implications. Here, we explore the underlying fine-scale genetic variations in the gut phageome, especially structural variations (SVs). By using virome-enriched long-read metagenomic sequencing across 91 individuals, we identified a total of 14,438 nonredundant phage SVs and revealed their prevalence within the human gut phageome. These SVs are mainly enriched in genes involved in recombination, DNA methylation, and antibiotic resistance. Notably, a substantial fraction of phage SV sequences share close homology with bacterial fragments, with most SVs enriched for horizontal gene transfer (HGT) mechanism. Further investigations showed that these SV sequences were genetic exchanged between specific phage-bacteria pairs, particularly between phages and their respective bacterial hosts. Temperate phages exhibit a higher frequency of genetic exchange with bacterial chromosomes and then virulent phages. Collectively, our findings provide insights into the genetic landscape of the human gut phageome.},
}
@article {pmid39141562,
year = {2024},
author = {Karan, J and Mandal, S and Khan, G and Arya, H and Samhita, L},
title = {Enhanced Extraction of Low-Molecular Weight DNA from Wastewater for Comprehensive Assessment of Antimicrobial Resistance.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {209},
pages = {},
doi = {10.3791/66899},
pmid = {39141562},
issn = {1940-087X},
mesh = {*Wastewater/microbiology/chemistry ; Polyethylene Glycols/chemistry ; Molecular Weight ; DNA, Bacterial/genetics/isolation &amp; purification ; Drug Resistance, Microbial/genetics ; Drug Resistance, Bacterial/genetics ; },
abstract = {Environmental surveillance is recognized as an important tool for assessing public health in the post-pandemic era. Water, in particular wastewater, has emerged as the source of choice to sample pathogen burdens in the environment. Wastewater from open drains and community water treatment plants is a reservoir of both pathogens and antimicrobial resistance (AMR) genes, and frequently comes in contact with humans. While there are many methods of tracking AMR from water, isolating good-quality DNA at high yields from heterogeneous samples remains a challenge. To compensate, sample volumes often need to be high, creating practical constraints. Additionally, environmental DNA is frequently fragmented, and the sources of AMR (plasmids, phages, linear DNA) consist of low-molecular-weight DNA. Yet, few extraction processes have focused on methods for high-yield extraction of linear and low-molecular-weight DNA. Here, a simple method for high-yield linear DNA extraction from small volumes of wastewater using the precipitation properties of polyethylene glycol (PEG) is reported. This study makes a case for increasing overall DNA yields from water samples collected for metagenomic analyses by enriching the proportion of linear DNA. In addition, enhancing low-molecular-weight DNA overcomes the current problem of under-sampling environmental AMR due to a focus on high-molecular-weight and intracellular DNA. This method is expected to be particularly useful when extracellular DNA exists but at low concentrations, such as with effluents from treatment plants. It should also enhance the environmental sampling of AMR gene fragments that spread through horizontal gene transfer.},
}
@article {pmid39140734,
year = {2024},
author = {Tian, Y and Rimal, B and Bisanz, JE and Gui, W and Wolfe, TM and Koo, I and Murray, IA and Nettleford, SK and Yokoyama, S and Dong, F and Koshkin, S and Prabhu, KS and Turnbaugh, PJ and Walk, ST and Perdew, GH and Patterson, AD},
title = {Effects of Early Life Exposures to the Aryl Hydrocarbon Receptor Ligand TCDF on Gut Microbiota and Host Metabolic Homeostasis in C57BL/6J Mice.},
journal = {Environmental health perspectives},
volume = {132},
number = {8},
pages = {87005},
pmid = {39140734},
issn = {1552-9924},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects/physiology ; *Receptors, Aryl Hydrocarbon/metabolism ; Mice ; *Mice, Inbred C57BL ; *Homeostasis/drug effects ; *Benzofurans ; Persistent Organic Pollutants ; Male ; Ligands ; },
abstract = {BACKGROUND: Exposure to persistent organic pollutants (POPs) and disruptions in the gastrointestinal microbiota have been positively correlated with a predisposition to factors such as obesity, metabolic syndrome, and type 2 diabetes; however, it is unclear how the microbiome contributes to this relationship.<br><br>OBJECTIVE: This study aimed to explore the association between early life exposure to a potent aryl hydrocarbon receptor (AHR) agonist and persistent disruptions in the microbiota, leading to impaired metabolic homeostasis later in life.<br><br>METHODS: This study used metagenomics, nuclear magnetic resonance (NMR)- and mass spectrometry (MS)-based metabolomics, and biochemical assays to analyze the gut microbiome composition and function, as well as the physiological and metabolic effects of early life exposure to 2,3,7,8-tetrachlorodibenzofuran (TCDF) in conventional, germ-free (GF), and Ahr-null mice. The impact of TCDF on Akkermansia muciniphila (A. muciniphila) in vitro was assessed using optical density (OD 600), flow cytometry, transcriptomics, and MS-based metabolomics.<br><br>RESULTS: TCDF-exposed mice exhibited lower abundances of A. muciniphila, lower levels of cecal short-chain fatty acids (SCFAs) and indole-3-lactic acid (ILA), as well as lower levels of the gut hormones glucagon-like peptide 1 (GLP-1) and peptide YY (PYY), findings suggestive of disruption in the gut microbiome community structure and function. Importantly, microbial and metabolic phenotypes associated with early life POP exposure were transferable to GF recipients in the absence of POP carry-over. In addition, AHR-independent interactions between POPs and the microbiota were observed, and they were significantly associated with growth, physiology, gene expression, and metabolic activity outcomes of A. muciniphila, supporting suppressed activity along the ILA pathway.<br><br>CONCLUSIONS: These data obtained in a mouse model point to the complex effects of POPs on the host and microbiota, providing strong evidence that early life, short-term, and self-limiting POP exposure can adversely impact the microbiome, with effects persisting into later life with associated health implications. https://doi.org/10.1289/EHP13356.},
}
@article {pmid39140417,
year = {2024},
author = {Hummel, G and Aagaard, K},
title = {Arthropods to Eutherians: A Historical and Contemporary Comparison of Sparse Prenatal Microbial Communities Among Animalia Species.},
journal = {American journal of reproductive immunology (New York, N.Y. : 1989)},
volume = {92},
number = {2},
pages = {e13897},
doi = {10.1111/aji.13897},
pmid = {39140417},
issn = {1600-0897},
mesh = {Animals ; Humans ; *Microbiota ; Pregnancy ; Female ; },
abstract = {Since the advent of next-generation sequencing, investigators worldwide have sought to discern whether a functional and biologically or clinically relevant prenatal microbiome exists. One line of research has led to the hypothesis that microbial DNA detected in utero/in ovo or prior to birth/hatching is a result of contamination and does not belong to viable and functional microbes. Many of these preliminary evaluations have been conducted in humans, mice, and nonhuman primates due to sample and specimen availability. However, a comprehensive review of the literature across animal species suggests organisms that maintain an obligate relationship with microbes may act as better models for interrogating the selective pressures placed on vertical microbial transfer over traditional laboratory species. To date, studies in humans and viviparous laboratory species have failed to illustrate the clear presence and transfer of functional microbes in utero. Until a ground truth regarding the status and relevance of prenatal microbes can be ascertained, it is salient to conduct parallel investigations into the prevalence of a functional prenatal microbiome across the developmental lifespan of multiple organisms in the kingdom Animalia. This comprehensive understanding is necessary not only to determine the role of vertically transmitted microbes and their products in early human health but also to understand their full One Health impact. This review is among the first to compile such comprehensive primary conclusions from the original investigator's conclusions, and hence collectively illustrates that prenatal microbial transfer is supported by experimental evidence arising from over a long and rigorous scientific history encompassing a breadth of species from kingdom Animalia.},
}
@article {pmid39139486,
year = {2024},
author = {Han, DM and Baek, JH and Choi, DG and Jeon, CO},
title = {Fermentative metabolic features of doenjang-meju as revealed by genome-centered metatranscriptomics.},
journal = {Food chemistry: X},
volume = {23},
number = {},
pages = {101658},
pmid = {39139486},
issn = {2590-1575},
abstract = {Fermentative features of doenjang-meju, a traditional Korean soybean brick, were investigated over 45 days via genome-centered metatranscriptomics. The pH value rapidly decreased within 10 days and successively increased after 20 days, along with an initial bacterial growth, including lactic acid bacteria, and subsequent fungal growth, suggesting their association. Polysaccharides and lipids underwent degradation, and amino acids, free sugars, and organic acids increased during the early stage. Metagenome analysis identified Aspergillus, Bacillus, Enterococcus, Staphylococcus, and Leuconostoc as major microbes, which were isolated and genome-sequenced. Metatranscriptomic analysis revealed the major roles of Bacillus and Enterococcus during the early period, shifting to Aspergillus dominance after 10 days. Metabolic pathway reconstruction and transcriptional analysis reveal that Aspergillus primarily decomposed polysaccharides to free sugars; Aspergillus and Bacillus metabolized lipids, free sugars, and organic acids generated by Enterococcus; and Aspergillus and Bacillus were instrumental in amino acid metabolism: their contributions varied by compounds and pathways.},
}
@article {pmid39139380,
year = {2024},
author = {Han, D and Bao, X and Wang, Y and Liao, X and Wang, K and Chen, J and Li, X and Yang, Z and Wang, Y},
title = {The impact of lactic acid bacteria inoculation on the fermentation and metabolomic dynamics of indigenous Beijing douzhi microbial communities.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1435834},
pmid = {39139380},
issn = {1664-302X},
abstract = {BACKGROUND: Douzhi, a traditional Chinese fermented beverage, features microbial communities primarily composed of lactic acid bacteria (LAB). As fermented foods continue to gain recognition and popularity, douzhi is attracting growing interest. However, investigation of the critical aspects of douzhi's fermentation processes, including fermentation characteristics and microbial community dynamics, remains vital for enhancing food safety and quality for douzhi, as well as for similar fermented food products.<br><br>METHOD: In this study, we collected douzhi microbial communities from four chain stores, using them as fermentation starter cultures. The microbial dynamics of the fermentation were analyzed, focusing on the inoculation of LAB strains and the transition from a mung bean-based matrix to skimmed milk. The metabolomic profiles of the fermented mung bean matrices were also studied.<br><br>RESULTS: Douzhi samples obtained from representative chain stores were found to be overwhelmingly dominated by LAB. When inoculated along with the douzhi community, both LAB strains exhibited notable and substantial reductions in the pH value of the designated mung bean matrices compared to those inoculated indigenous microbiota. Specifically, Lactiplantibacillus plantarum CGMCC 1.1856 retained its population, whereas Pediococcus pentosaceus CGMCC 1.2695 exhibited a decrease in relative abundance. Using skimmed milk as a fermentation substrate instead of the mung bean matrix resulted in significant shifts in microbial communities, particularly leading to an increase in Escherichia sp. The metagenomic analyses and functional predictions illustrated that various metabolic functions were enhanced during the fermentation process due to LAB inoculation. The liquid chromatography-mass spectrometry based metabolomic analysis revealed that the inoculation of Lactiplantibacillus plantarum and Pediococcus pentosaceus in mung bean matrix did not introduce new metabolites but significantly altered the concentration and profile of existing metabolites, especially increased low molecular carbohydrates, which may enhance the nutritional potential of the fermented product.<br><br>DISCUSSION: This study examines the microbial dynamics of douzhi microbiota fermentation, emphasizing the role of lactic acid bacteria in enhancing fermentation activity and metabolite profiles. These insights contribute to improving manufacturing processes and ensuring the safety and quality of douzhi and similar fermented foods.},
}
@article {pmid39139377,
year = {2024},
author = {Murovec, B and Deutsch, L and Osredkar, D and Stres, B},
title = {MetaBakery: a Singularity implementation of bioBakery tools as a skeleton application for efficient HPC deconvolution of microbiome metagenomic sequencing data to machine learning ready information.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1426465},
pmid = {39139377},
issn = {1664-302X},
abstract = {In this study, we present MetaBakery (http://metabakery.fe.uni-lj.si), an integrated application designed as a framework for synergistically executing the bioBakery workflow and associated utilities. MetaBakery streamlines the processing of any number of paired or unpaired fastq files, or a mixture of both, with optional compression (gzip, zip, bzip2, xz, or mixed) within a single run. MetaBakery uses programs such as KneadData (https://github.com/bioBakery/kneaddata), MetaPhlAn, HUMAnN and StrainPhlAn as well as integrated utilities and extends the original functionality of bioBakery. In particular, it includes MelonnPan for the prediction of metabolites and Mothur for calculation of microbial alpha diversity. Written in Python 3 and C++ the whole pipeline was encapsulated as Singularity container for efficient execution on various computing infrastructures, including large High-Performance Computing clusters. MetaBakery facilitates crash recovery, efficient re-execution upon parameter changes, and processing of large data sets through subset handling and is offered in three editions with bioBakery ingredients versions 4, 3 and 2 as versatile, transparent and well documented within the MetaBakery Users' Manual (http://metabakery.fe.uni-lj.si/metabakery_manual.pdf). It provides automatic handling of command line parameters, file formats and comprehensive hierarchical storage of output to simplify navigation and debugging. MetaBakery filters out potential human contamination and excludes samples with low read counts. It calculates estimates of alpha diversity and represents a comprehensive and augmented re-implementation of the bioBakery workflow. The robustness and flexibility of the system enables efficient exploration of changing parameters and input datasets, increasing its utility for microbiome analysis. Furthermore, we have shown that the MetaBakery tool can be used in modern biostatistical and machine learning approaches including large-scale microbiome studies.},
}
@article {pmid39139260,
year = {2024},
author = {Zawadzki, R and Rogalska, W and Pałdyna, M and Głuszczuk, D and Zajkowska, J and Kubas, B},
title = {Imaging modalities in neurolisteriosis: a literature review.},
journal = {Polish journal of radiology},
volume = {89},
number = {},
pages = {e345-e357},
pmid = {39139260},
issn = {1733-134X},
abstract = {Listeriosis caused by Listeria monocytogenes due to its ability to withstand harsh conditions and form biofilms on post-processed food poses a serious public health issue. It typically manifests itself with fever and gastrointestinal symptoms, but it can escalate with life-threatening conditions, especially in immunocompromised patients, the elderly, oncologically sick, and even pregnant women. The diagnosis is based on blood and cerebrospinal fluid culture growth, but it presents significant challenges due to deceptive findings and low positivity rates, the golden standard includes molecular diagnostic tests such as real-time PCR and metagenomic next-generation sequencing, which offer higher sensitivity and rapid detection. Radiological imaging, particularly magnetic resonance imaging, can play a crucial role in diagnosis of central nervous system (CNS) invasion by L. monocytogenes, enabling the detection of characteristic CNS lesions. The aim of the paper was to sum up the imaging features of L. monocytogenes CNS invasions in conventional imaging techniques, which can potentially speed up the diagnostic workflow for patients presenting with neurological symptoms associated with L. monocytogenes infection, particularly when conventional tests yield inconclusive results.},
}
@article {pmid39139158,
year = {2024},
author = {Zeng, W and Liang, Y and He, X and Chen, F and Xiong, J and Wen, Z and Tang, L and Chen, X and Zhang, J},
title = {Exploring the pathogen diagnosis and prognostic factors of severe COVID-19 using metagenomic next-generation sequencing: A retrospective study.},
journal = {Journal of medical biochemistry},
volume = {43},
number = {4},
pages = {528-536},
pmid = {39139158},
issn = {1452-8258},
abstract = {BACKGROUND: This study aimed to identify pathogens and factors that predict the outcome of severe COVID-19 by utilizing metagenomic next-generation sequencing (mNGS) technology.<br><br>METHODS: We retrospectively analyzed data from 56 severe COVID-19 patients admitted to our hospital between December 2022 and March 2023. We analyzed the pathogen types and strains detected through mNGS and conventional microbiological testing and collected general patient information.<br><br>RESULTS: In this study, 42 pathogens were detected using mNGS and conventional microbiological testing. mNGS had a significantly higher detection rate of 90.48% compared to 71.43% for conventional testing (P=0.026). A total of 196 strains were detected using both methods, with a significantly higher detection rate of 70.92% for mNGS compared to 49.49% for conventional testing (P=0.000). The 56 patients were divided into a survival group (33 cases) and a death group (23 cases) based on clinical outcomes. The survival group had significantly lower age, number of pathogens detected by mNGS, number of pathogens detected by conventional testing, APACHE-II score, SOFA score, high-sensitivity troponin, creatine kinase-MB subtype, and lactate dehydrogenase compared to the death group (P<0.05). Multivariate logistic regression analysis showed that these factors were risk factors for mortality in severe COVID-19 patients (P<0.05). In contrast, ROC curve analysis revealed that these factors had diagnostic values for mortality, with AUC values ranging from 0.657 to 0.963. The combined diagnosis of these indicators had an AUC of 0.924.<br><br>CONCLUSIONS: The use of mNGS technology can significantly enhance the detection of pathogens in severe cases of COVID-19 and also has a solid ability to predict clinical outcomes.},
}
@article {pmid39138687,
year = {2024},
author = {Singh, A and T V, A and Singh, S and Saxena, AK and Nain, L},
title = {Application of fungal inoculants enhances colonization of secondary bacterial degraders during in situ paddy straw degradation: a genomic insights into cross-domain synergism.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {39138687},
issn = {1618-1905},
support = {2017-20//ICAR-AMAAS/ ; },
abstract = {Rice cultivation generates huge amounts of on farm residues especially under mechanical harvesting. Paddy straw being recalcitrant hinders sowing of upcoming rabi crops like wheat and mustard. Non-environmental sustainable practice of on-farm burning of the paddy residues is being popularly followed for quick disposal of the agro-residues and land preparation. However, conservation agriculture involving in situ residue incorporation can be a sustainable option to utilize the residues for improvement of soil biological health. However, low temperature coupled with poor nitrogen status of soil reduces the decomposition rate of residues that may lead to nitrogen immobilization and hindrance in land preparation. In this direction, ecological impact of two approaches viz priming with urea and copiotrophic fungus-based bioformulation (CFB) consisting of Coprinopsis cinerea LA2 and Cyathus stercoreus ITCC3745 was studied for in situ degradation of residues. Succession of bacterial diversity was deciphered through high throughput whole metagenomic sequencing along with studies on dynamics of soil microbial enzymes. Treatments receiving CFB (T1) and urea (T2) when compared with bulk soil (absolute control) showed an increase in richness of the microbial diversity as compared to control straw retained treatment control (T3). The β diversity indices also indicated sufficient group variations among the treatments receiving CFB and urea as compared to only straw retained treatment and bulk soil. Priming of paddy straw with CFB and urea also induced significant rewiring of the bacterial co-occurrence networks. Quantification of soil ligno-cellulolytic activity as well as abundance of carbohydrate active enzymes (CAZy) genes indicated high activities of hydrolytic enzymes in CFB primed straw retention treatment as compared to urea primed straw retention treatment. The genomic insights on effectiveness of copiotrophic fungus bioformulation for in situ degradation of paddy straw will further help in developing strategies for management of crop residues in eco-friendly manner.},
}
@article {pmid39138568,
year = {2024},
author = {Belda, E and Capeau, J and Zucker, JD and Chatelier, EL and Pons, N and Oñate, FP and Quinquis, B and Alili, R and Fellahi, S and Katlama, C and Clément, K and Fève, B and Jaureguiberry, S and Goujard, C and Lambotte, O and Doré, J and Prifti, E and Bastard, JP},
title = {Major depletion of insulin sensitivity-associated taxa in the gut microbiome of persons living with HIV controlled by antiretroviral drugs.},
journal = {BMC medical genomics},
volume = {17},
number = {1},
pages = {209},
pmid = {39138568},
issn = {1755-8794},
support = {ANRS 157 study trial//Agence Nationale de Recherches sur le Sida et les H&#xe9;patites Virales/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *HIV Infections/drug therapy/microbiology ; Male ; Female ; Middle Aged ; *Insulin Resistance ; Adult ; Feces/microbiology ; Anti-Retroviral Agents/therapeutic use ; Metagenome ; },
abstract = {BACKGROUND: Persons living with HIV (PWH) harbor an altered gut microbiome (higher abundance of Prevotella and lower abundance of Bacillota and Ruminococcus lineages) compared to non-infected individuals. Some of these alterations are linked to sexual preference and others to the HIV infection. The relationship between these lineages and metabolic alterations, often present in aging PWH, has been poorly investigated.<br><br>METHODS: In this study, we compared fecal metagenomes of 25 antiretroviral-treatment (ART)-controlled PWH to three independent control groups of 25 non-infected matched individuals by means of univariate analyses and machine learning methods. Moreover, we used two external datasets to validate predictive models of PWH classification. Next, we searched for associations between clinical and biological metabolic parameters with taxonomic and functional microbiome profiles. Finally, we compare the gut microbiome in 7 PWH after a 17-week ART switch to raltegravir/maraviroc.<br><br>RESULTS: Three major enterotypes (Prevotella, Bacteroides and Ruminococcaceae) were present in all groups. The first Prevotella enterotype was enriched in PWH, with several of characteristic lineages associated with poor metabolic profiles (low HDL and adiponectin, high insulin resistance (HOMA-IR)). Conversely butyrate-producing lineages were markedly depleted in PWH independently of sexual preference and were associated with a better metabolic profile (higher HDL and adiponectin and lower HOMA-IR). Accordingly with the worst metabolic status of PWH, butyrate production and amino-acid degradation modules were associated with high HDL and adiponectin and low HOMA-IR. Random Forest models trained to classify PWH vs. control on taxonomic abundances displayed high generalization performance on two external holdout datasets (ROC AUC of 80-82%). Finally, no significant alterations in microbiome composition were observed after switching to raltegravir/maraviroc.<br><br>CONCLUSION: High resolution metagenomic analyses revealed major differences in the gut microbiome of ART-controlled PWH when compared with three independent matched cohorts of controls. The observed marked insulin resistance could result both from enrichment in Prevotella lineages, and from the depletion in species producing butyrate and involved into amino-acid degradation, which depletion is linked with the HIV infection.},
}
@article {pmid39138557,
year = {2024},
author = {Lu, Y and Li, Q and Li, T},
title = {A novel hierarchical network-based approach to unveil the complexity of functional microbial genome.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {786},
pmid = {39138557},
issn = {1471-2164},
support = {2020YFA0907402//National Key Research and Development Program of China/ ; 92251304//National Natural Science Foundation of China/ ; },
mesh = {*Microcystis/genetics ; *Genome, Bacterial ; Lakes/microbiology ; Gene Regulatory Networks ; Metagenomics/methods ; Metagenome ; Genome, Microbial ; Genomics/methods ; Deep Learning ; },
abstract = {Biological networks serve a crucial role in elucidating intricate biological processes. While interspecies environmental interactions have been extensively studied, the exploration of gene interactions within species, particularly among individual microorganisms, is less developed. The increasing amount of microbiome genomic data necessitates a more nuanced analysis of microbial genome structures and functions. In this context, we introduce a complex structure using higher-order network theory, "Solid Motif Structures (SMS)", via a hierarchical biological network analysis of genomes within the same genus, effectively linking microbial genome structure with its function. Leveraging 162 high-quality genomes of Microcystis, a key freshwater cyanobacterium within microbial ecosystems, we established a genome structure network. Employing deep learning techniques, such as adaptive graph encoder, we uncovered 27 critical functional subnetworks and their associated SMSs. Incorporating metagenomic data from seven geographically distinct lakes, we conducted an investigation into Microcystis' functional stability under varying environmental conditions, unveiling unique functional interaction models for each lake. Our work compiles these insights into an extensive resource repository, providing novel perspectives on the functional dynamics within Microcystis. This research offers a hierarchical network analysis framework for understanding interactions between microbial genome structures and functions within the same genus.},
}
@article {pmid39137850,
year = {2024},
author = {Kou, L and Huang, T and Zhang, H and Wen, G and Li, K},
title = {Aerobic denitrifying bacterial community with low C/N ratio remove nitrate from micro-polluted water: Metagenomics unravels denitrification pathways.},
journal = {The Science of the total environment},
volume = {951},
number = {},
pages = {175457},
doi = {10.1016/j.scitotenv.2024.175457},
pmid = {39137850},
issn = {1879-1026},
mesh = {*Denitrification ; *Nitrates/metabolism ; *Water Pollutants, Chemical/metabolism/analysis ; *Nitrogen/metabolism ; *Metagenomics ; *Carbon/metabolism ; Bacteria/metabolism ; Aerobiosis ; Biodegradation, Environmental ; },
abstract = {The efficient nitrogen removal from micro-polluted source water is an international challenge to be solved urgently. However, the inner denitrification mechanism of native aerobic denitrifying bacterial communities in response to carbon scarcity remains relatively unclear. Here, the bacterial community XT6, screened from an oligotrophic reservoir, exhibited aerobic denitrifying capacity under low-carbon environments. Up to 76.79-81.64 % of total organic carbon (TOC) and 51.48-67.60 % of NO3[-]-N were removed by XT6 within 48 h at C/N ratios of 2.0-3.0. Additionally, the nitrogen balance experiments further manifested that 26.27-38.13 % of NO3[-]-N was lost in gaseous form. As the C/N ratio decreased, XT6 tended to generate more extracellular polymeric substances (EPS), with the tightly bound EPS showing the largest increase. Pseudomonas and Variovorax were quite abundant in XT6, constituting 59.69 % and 28.65 % of the total sequences, respectively. Furthermore, metagenomics analysis evidenced that XT6 removed TOC and nitrate mainly through the tricarboxylic acid cycle and aerobic denitrification. Overall, the abovementioned results provide a deeper understanding of the nitrogen metabolic pathways of indigenous aerobic denitrifying bacterial communities with low C/N ratios and offer useful guidance for controlling nitrogen pollution in oligotrophic ecosystems.},
}
@article {pmid39137667,
year = {2024},
author = {Ma, ZS},
title = {Metagenome comparison (MC): A new framework for detecting unique/enriched OMUs (operational metagenomic units) derived from whole-genome sequencing reads.},
journal = {Computers in biology and medicine},
volume = {180},
number = {},
pages = {108852},
doi = {10.1016/j.compbiomed.2024.108852},
pmid = {39137667},
issn = {1879-0534},
mesh = {Humans ; *Metagenomics/methods ; *Metagenome/genetics ; Whole Genome Sequencing/methods ; Algorithms ; },
abstract = {BACKGROUND: Current methods for comparing metagenomes, derived from whole-genome sequencing reads, include top-down metrics or parametric models such as metagenome-diversity, and bottom-up, non-parametric, model-free machine learning approaches like Naïve Bayes for k-mer-profiling. However, both types are limited in their ability to effectively and comprehensively identify and catalogue unique or enriched metagenomic genes, a critical task in comparative metagenomics. This challenge is significant and complex due to its NP-hard nature, which means computational time grows exponentially, or even faster, with the problem size, rendering it impractical for even the fastest supercomputers without heuristic approximation algorithms.<br><br>METHOD: In this study, we introduce a new framework, MC (Metagenome-Comparison), designed to exhaustively detect and catalogue unique or enriched metagenomic genes (MGs) and their derivatives, including metagenome functional gene clusters (MFGC), or more generally, the operational metagenomic unit (OMU) that can be considered the counterpart of the OTU (operational taxonomic unit) from amplicon sequencing reads. The MC is essentially a heuristic search algorithm guided by pairs of new metrics (termed MG-specificity or OMU-specificity, MG-specificity diversity or OMU-specificity diversity). It is further constrained by statistical significance (P-value) implemented as a pair of statistical tests.<br><br>RESULTS: We evaluated the MC using large metagenomic datasets related to obesity, diabetes, and IBD, and found that the proportions of unique and enriched metagenomic genes ranged from 0.001% to 0.08&#xa0;% and 0.08%-0.82&#xa0;% respectively, and less than 10&#xa0;% for the MFGC.<br><br>CONCLUSION: The MC provides a robust method for comparing metagenomes at various scales, from baseline MGs to various function/pathway clusters of metagenomes, collectively termed OMUs.},
}
@article {pmid39137550,
year = {2024},
author = {Gao, SM and Wang, P and Li, Q and Shu, WS and Tang, LY and Lin, ZL and Li, JT and Huang, LN},
title = {Deciphering microbial metabolic interactions and their implications for community dynamics in acid mine drainage sediments.},
journal = {Journal of hazardous materials},
volume = {478},
number = {},
pages = {135478},
doi = {10.1016/j.jhazmat.2024.135478},
pmid = {39137550},
issn = {1873-3336},
mesh = {*Geologic Sediments/microbiology ; *Mining ; *Microbiota ; *Biodegradation, Environmental ; Bacteria/metabolism/genetics ; China ; Metagenomics ; Acids/metabolism ; Microbial Interactions ; },
abstract = {The microbially-mediated reduction processes have potential for the bioremediation of acid mine drainage (AMD), which represents a worldwide environment problem. However, we know little about the microbial interactions in anaerobic AMD sediments. Here we utilized genome-resolved metagenomics to uncover the nature of cooperative and competitive metabolic interactions in 90 AMD sediments across Southern China. Our analyses recovered well-represented prokaryotic communities through the reconstruction of 2625 population genomes. Functional analyses of these genomes revealed extensive metabolic handoffs which occurred more frequently in nitrogen metabolism than in sulfur metabolism, as well as stable functional redundancy across sediments resulting from populations with low genomic relatedness. Genome-scale metabolic modeling showed that metabolic competition promoted microbial co-occurrence relationships, suggesting that community assembly was dominated by habitat filtering in sediments. Notably, communities colonizing more extreme conditions tended to be highly competitive, which was typically accompanied with increased network complexity but decreased stability of the microbiome. Finally, our results demonstrated that heterotrophic Thermoplasmatota associated with ferric iron and sulfate reduction contributed most to the elevated levels of competition. Our study shed light on the cooperative and competitive metabolisms of microbiome in the hazardous AMD sediments, which may provide preliminary clues for the AMD bioremediation in the future.},
}
@article {pmid39137456,
year = {2024},
author = {Li, J and Yang, W and Hao, X and Lin, Y and van Loosdrecht, MCM},
title = {Little alginates synthesized in EPS: Evidences from high-throughput community and metagenes.},
journal = {Water research},
volume = {265},
number = {},
pages = {122211},
doi = {10.1016/j.watres.2024.122211},
pmid = {39137456},
issn = {1879-2448},
mesh = {*Alginates ; *Extracellular Polymeric Substance Matrix/metabolism ; Sewage/microbiology ; Bacteria/metabolism/genetics ; Bioreactors ; },
abstract = {As a significant structure in activated sludge, extracellular polymeric substances (EPS) hold considerable value regarding resource recovery and applications. The present study aimed to elucidate the relationship between the microbial community and the composition and properties of EPS. A biological nutrient removal (BNR) reactor was set up in the laboratory and controlled under different solid retention times (SRT), altering microbial species within the system. Then EPS was extracted from activated and analyzed by chemical and spectroscopic methods. High-throughput sequencing and metagenomic approaches were employed to investigate bacterial community and metabolic pathways. The results showed that lower SRT with a higher abundance of the family-level Proteobacteria (27.7%-53.5%) favored EPS synthesis, while another dominant group Bacteroidetes (20.0%-32.6%) may not significantly affect EPS synthesis. Furthermore, the abundance of alginates-producing bacteria including Pseudomonas spp. and Azotobacter vinelandii was only 2.53%-6.76% and 1.98%-6.34%, respectively. The alginate synthesis pathway genes Alg8 and Alg44 were also present at very low levels (0.05‱-0.11‱, 0.01‱-0.02‱, respectively). Another important gene related to alginates operons, AlgK, was absent across all the SRT-operated reactors. These findings suggest an impossible and incomplete alginate synthesis pathway within sludge. In light of these results, it can be concluded that EPS does not necessarily contain alginate components.},
}
@article {pmid39137184,
year = {2024},
author = {Tang, X and Shang, J and Chen, G and Chan, KHK and Shi, M and Sun, Y},
title = {SegVir: Reconstruction of Complete Segmented RNA Viral Genomes from Metatranscriptomes.},
journal = {Molecular biology and evolution},
volume = {41},
number = {8},
pages = {},
pmid = {39137184},
issn = {1537-1719},
mesh = {*Genome, Viral ; *RNA Viruses/genetics ; Transcriptome ; RNA, Viral/genetics ; Software ; Metagenome ; Metagenomics/methods ; },
abstract = {Segmented RNA viruses are a complex group of RNA viruses with multisegment genomes. Reconstructing complete segmented viruses is crucial for advancing our understanding of viral diversity, evolution, and public health impact. Using metatranscriptomic data to identify known and novel segmented viruses has sped up the survey of segmented viruses in various ecosystems. However, the high genetic diversity and the difficulty in binning complete segmented genomes present significant challenges in segmented virus reconstruction. Current virus detection tools are primarily used to identify nonsegmented viral genomes. This study presents SegVir, a novel tool designed to identify segmented RNA viruses and reconstruct their complete genomes from complex metatranscriptomes. SegVir leverages both close and remote homology searches to accurately detect conserved and divergent viral segments. Additionally, we introduce a new method that can evaluate the genome completeness and conservation based on gene content. Our evaluations on simulated datasets demonstrate SegVir's superior sensitivity and precision compared to existing tools. Moreover, in experiments using real data, we identified some virus segments missing in the NCBI database, underscoring SegVir's potential to enhance viral metagenome analysis. The source code and supporting data of SegVir are available via https://github.com/HubertTang/SegVir.},
}
@article {pmid39136809,
year = {2024},
author = {Kulshreshtha, NM and Chauhan, K and Singh, A and Soti, A and Kumari, M and Gupta, AB},
title = {Intertwining of the C-N-S cycle in passive and aerated constructed wetlands.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {40},
number = {10},
pages = {301},
pmid = {39136809},
issn = {1573-0972},
support = {DST/TM/WTI/WIC/2K17/83//Department of Science and Technology, Ministry of Science and Technology, India/ ; },
mesh = {*Wetlands ; *Bacteria/metabolism/classification/genetics/isolation &amp; purification ; *Nitrogen/metabolism ; *Denitrification ; *Sulfur/metabolism ; Carbon/metabolism ; Autotrophic Processes ; Carbon Cycle ; Wastewater/microbiology/chemistry ; Metagenomics ; },
abstract = {The microbial processes occurring in constructed wetlands (CWs) are difficult to understand owing to the complex interactions occurring between a variety of substrates, microorganisms, and plants under the given physicochemical conditions. This frequently leads to very large unexplained nitrogen losses in these systems. In continuation of our findings on Anammox contributions, our research on full-scale field CWs has suggested the significant involvement of the sulfur cycle in the conventional C-N cycle occurring in wetlands, which might closely explain the nitrogen losses in these systems. This paper explored the possibility of the sulfur-driven autotrophic denitrification (SDAD) pathway in different types of CWs, shallow and deep and passive and aerated systems, by analyzing the metagenomic bacterial communities present within these CWs. The results indicate a higher abundance of SDAD bacteria (Paracoccus and Arcobacter) in deep passive systems compared to shallow systems and presence of a large number of SDAD genera (Paracoccus, Thiobacillus, Beggiatoa, Sulfurimonas, Arcobacter, and Sulfuricurvum) in aerated CWs. The bacteria belonging to the functional category of dark oxidation of sulfur compounds were found to be enriched in deep and aerated CWs hinting at the possible role of the SDAD pathway in total nitrogen removal in these systems. As a case study, the percentage nitrogen removal through SDAD pathway was calculated to be 15-20% in aerated wetlands. The presence of autotrophic pathways for nitrogen removal can prove highly beneficial in terms of reducing sludge generation and hence reducing clogging, making aerated CWs a sustainable wastewater treatment solution.},
}
@article {pmid39136491,
year = {2024},
author = {Schacksen, PS and Nielsen, JL},
title = {Unraveling the genetic potential of nitrous oxide reduction in wastewater treatment: insights from metagenome-assembled genomes.},
journal = {Applied and environmental microbiology},
volume = {90},
number = {9},
pages = {e0217723},
pmid = {39136491},
issn = {1098-5336},
support = {9041-00367B//Teknologi og Produktion, Det Frie Forskningsr&#xe5;d (FTP, DFF)/ ; },
mesh = {*Nitrous Oxide/metabolism ; *Wastewater/microbiology ; *Metagenome ; Bacteria/genetics/metabolism/classification/isolation &amp; purification ; Oxidation-Reduction ; Oxidoreductases/genetics/metabolism ; Genome, Bacterial ; Waste Disposal, Fluid ; Denmark ; Phylogeny ; },
abstract = {UNLABELLED: This study explores the genetic landscape of nitrous oxide (N2O) reduction in wastewater treatment plants (WWTPs) by profiling 1,083 high-quality metagenome-assembled genomes (HQ MAGs) from 23 Danish full-scale WWTPs. The focus is on the distribution and diversity of nitrous oxide reductase (nosZ) genes and their association with other nitrogen metabolism pathways. A custom pipeline for clade-specific nosZ gene identification with higher sensitivity revealed 503 nosZ sequences in 489 of these HQ MAGs, outperforming existing Kyoto Encyclopedia of Genes and Genomes (KEGG) module-based methods. Notably, 48.7% of the total 1,083 HQ MAGs harbored nosZ genes, with clade II being predominant, accounting for 93.7% of these genes. Taxonomic profiling highlighted the prevalence of nosZ-containing taxa within Bacteroidota and Pseudomonadota. Chloroflexota exhibited unexpected affiliations with both the sec and tat secretory pathways, and all were found to contain the accessory nosB gene, underscoring the importance of investigating the secretory pathway. The majority of non-denitrifying N2O reducers were found within Bacteroidota and Chloroflexota. Additionally, HQ MAGs with genes for dissimilatory nitrate reduction to ammonium and assimilatory nitrate reduction frequently co-occurred with the nosZ gene. Traditional primers targeting nosZ often focus on short-length amplicons. Therefore, we introduced custom-designed primer sets targeting near-full-length nosZ sequences. These new primers demonstrate efficacy in capturing diverse and well-characterized sequences, providing a valuable tool with higher resolution for future research. In conclusion, this comprehensive analysis enhances our understanding of N2O-reducing organisms in WWTPs, highlighting their potential as N2O sinks with the potential for optimizing wastewater treatment processes and mitigating greenhouse gas emissions.<br><br>IMPORTANCE: This study provides critical insights into the genetic diversity of nitrous oxide reductase (nosZ) genes and the microorganisms harboring them in wastewater treatment plants (WWTPs) by exploring 1,083 high-quality metagenome-assembled genomes (MAGs) from 23 Danish full-scale WWTPs. Despite the pivotal role of nosZ-containing organisms, their diversity remains largely unexplored in WWTPs. Our custom pipeline for detecting nosZ provides near-full-length genes with detailed information on secretory pathways and accessory nos genes. Using these genes as templates, we developed taxonomically diverse clade-specific primers that generate nosZ amplicons for phylogenetic annotation and gene-to-MAG linkage. This approach improves detection and expands the discovery of novel sequences, highlighting the prevalence of non-denitrifying N2O reducers and their potential as N2O sinks. These findings have the potential to optimize nitrogen removal processes and mitigate greenhouse gas emissions from WWTPs by fully harnessing the capabilities of the microbial communities.},
}
@article {pmid39136455,
year = {2024},
author = {Majzoub, ME and Luu, LDW and Haifer, C and Paramsothy, S and Borody, TJ and Leong, RW and Thomas, T and Kaakoush, NO},
title = {Refining microbial community metabolic models derived from metagenomics using reference-based taxonomic profiling.},
journal = {mSystems},
volume = {9},
number = {9},
pages = {e0074624},
pmid = {39136455},
issn = {2379-5077},
support = {988415//Crohn's and Colitis Foundation (CCF)/ ; 2011047//DHAC | National Health and Medical Research Council (NHMRC)/ ; //Bioplatforms Australia (Bioplatforms)/ ; //Integrated Marine Observing System (IMOS)/ ; Emerging leader grant//DHAC | National Health and Medical Research Council (NHMRC)/ ; Scientia fellowship//University of New South Wales (UNSW)/ ; },
mesh = {Humans ; *Metagenomics/methods ; *Metabolomics/methods ; *Microbiota/genetics ; Metagenome/genetics ; },
abstract = {Characterization of microbial community metabolic output is crucial to understanding their functions. Construction of genome-scale metabolic models from metagenome-assembled genomes (MAG) has enabled prediction of metabolite production by microbial communities, yet little is known about their accuracy. Here, we examined the performance of two approaches for metabolite prediction from metagenomes, one that is MAG-guided and another that is taxonomic reference-guided. We applied both on shotgun metagenomics data from human and environmental samples, and validated findings in the human samples using untargeted metabolomics. We found that in human samples, where taxonomic profiling is optimized and reference genomes are readily available, when number of input taxa was normalized, the reference-guided approach predicted more metabolites than the MAG-guided approach. The two approaches showed significant overlap but each identified metabolites not predicted in the other. Pathway enrichment analyses identified significant differences in inferences derived from data based on the approach, highlighting the need for caution in interpretation. In environmental samples, when the number of input taxa was normalized, the reference-guided approach predicted more metabolites than the MAG-guided approach for total metabolites in both sample types and non-redundant metabolites in seawater samples. Nonetheless, as was observed for the human samples, the approaches overlapped substantially but also predicted metabolites not observed in the other. Our findings report on utility of a complementary input to genome-scale metabolic model construction that is less computationally intensive forgoing MAG assembly and refinement, and that can be applied on shallow shotgun sequencing where MAGs cannot be generated.IMPORTANCELittle is known about the accuracy of genome-scale metabolic models (GEMs) of microbial communities despite their influence on inferring community metabolic outputs and culture conditions. The performance of GEMs for metabolite prediction from metagenomes was assessed by applying two approaches on shotgun metagenomics data from human and environmental samples, and validating findings in the human samples using untargeted metabolomics. The performance of the approach was found to be dependent on sample type, but collectively, the reference-guided approach predicted more metabolites than the MAG-guided approach. Despite the differences, the predictions from the approaches overlapped substantially but each identified metabolites not predicted in the other. We found significant differences in biological inferences based on the approach, with some examples of uniquely enriched pathways in one group being invalidated when using the alternative approach, highlighting the need for caution in interpretation of GEMs.},
}
@article {pmid39136189,
year = {2024},
author = {Wang, J and Zhu, YG and Ge, Y},
title = {Global distribution pattern of soil phosphorus-cycling microbes under the influence of human activities.},
journal = {Global change biology},
volume = {30},
number = {8},
pages = {e17477},
doi = {10.1111/gcb.17477},
pmid = {39136189},
issn = {1365-2486},
support = {2023YFD1700803//National Key Research and Development Program of China/ ; 42177274//National Natural Science Foundation of China/ ; 42307162//National Natural Science Foundation of China/ ; 2019QZKK0306//the Second Tibetan Plateau Scientific Expedition and Research Program/ ; 2019QZKK0308//the Second Tibetan Plateau Scientific Expedition and Research Program/ ; },
mesh = {*Phosphorus/metabolism/analysis ; *Soil Microbiology ; Human Activities ; Humans ; Bacteria/genetics/metabolism ; Microbiota ; Soil/chemistry ; },
abstract = {Human activities have profoundly altered the Earth's phosphorus (P) cycling process and its associated microbial communities, yet their global distribution pattern and response to human influences remain unclear. Here, we estimated the abundances of P-cycling genes from 3321 global soil metagenomic samples and mapped the global distribution of five key P-cycling processes, that is, organic phosphoester hydrolysis, inorganic phosphorus solubilization, two-component system, phosphotransferase system, and transporters. Structural equation modeling and random forest analysis were employed to assess the impact of anthropogenic and environmental factors on the abundance of P-cycling genes. Our findings suggest that although less significant than the climate and soil profile, human-related factors, such as economic activities and population, are important drivers for the variations in P-cycling gene abundance. Notably, the gene abundances were increased parallel to the extent of human intervention, but generally at low and moderate levels of human activities. Furthermore, we identified critical genera, such as Pseudomonas and Lysobacter, which were sensitive to the changes in human activities. This study provides insights into the responses of P-cycling microbes to human activities at a global scale, enhancing our understanding of soil microbial P cycling and underscoring the importance of sustainable human activities in the Earth's biogeochemical cycle.},
}
@article {pmid39135873,
year = {2024},
author = {Zhang, H and Wei, T and Li, Q and Fu, L and Li, M and He, L and Wang, Y},
title = {Metagenomic 18S rDNA reads revealed zonation of eukaryotic communities in the Yongle blue hole.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1420899},
pmid = {39135873},
issn = {1664-302X},
abstract = {The Yongle blue hole (YBH), situated in the South China Sea, represents a compelling subject of study in marine microbiology due to its unique redox-layered microbial ecosystems. However, the diversity and ecology of microbial eukaryotes within the YBH remains underexplored. This study endeavors to bridge this gap through the application of the in situ microbial filtration and fixation (ISMIFF) device to collect 0.22-30 μm microbial samples from 21 water layers of YBH. Subsequent extraction of 18S rRNA metagenomic reads of 21 metagenomes and 10 metatranscriptomes facilitated a comprehensive analysis of community structures. Findings revealed a pronounced superiority in the diversity and richness of eukaryotic microorganisms in the oxic zone compared to its suboxic and anoxic counterparts. Notably, Dinophyceae and Maxillopoda emerged as the predominant taxa based on the analysis of the 18S rRNA reads for the V4 and V9 regions, which showed stratification In their relative abundance and suggested their potential role in the thermo-halocline boundaries and oxic-anoxic interface. Specifically, In these eukaryotic microbial communities, Dinophyceae exhibited significant abundance at 20 m (20.01%) and 105 m (26.13%) water depths, while Maxillopoda was prevalent at 40 m (22.84%), 80 m (23.19%), and 100 m (15.42%) depths. A part of these organisms, identified as larvae and protists, were likely attracted by swarming chemosynthetic bacterial prey prevailing at the thermo-halocline boundaries and oxic-anoxic interface. Furthermore, the phylogenetic relationships of the major 18S operational taxonomic units (OTUs) showed a close adjacency to known species, except for three Dinophyceae OTUs. In conclusion, this study provides critical insights into the vertical distribution and transcriptional activity of <30-μm eukaryotic microbes, shedding light on the taxonomic novelty of eukaryotic microorganisms within the semi-enclosed blue holes.},
}
@article {pmid39135694,
year = {2024},
author = {Yu, J and Li, W and Xu, R and Liu, X and Gao, G and Kwok, LY and Chen, Y and Sun, Z and Liu, W and Zhang, H},
title = {Probio-M9, a breast milk-originated probiotic, alleviates mastitis and enhances antibiotic efficacy: Insights into the gut-mammary axis.},
journal = {iMeta},
volume = {3},
number = {4},
pages = {e224},
pmid = {39135694},
issn = {2770-596X},
abstract = {Breast milk naturally contains lactic acid bacteria, but their precise origin remains a subject of debate. In this study, we utilized a rat mastitis animal model to investigate the potential of a breast milk-derived probiotic strain, Lacticaseibacillus rhamnosus Probio-M9, in alleviating mastitis and enhancing the efficacy of antibiotic treatment. Through histopathological analysis of mammary tissue, we observed that Probio-M9 effectively relieved mastitis, mitigated inflammation, and improved the response to antibiotic treatment. Metagenomic analysis further revealed that Probio-M9 enhanced interactions among gut microbes, accompanied by an increase in the relative abundance of Ruminococcaceae and the regulation of specific genes and carbohydrate-active enzymes, subsequently impacting host immunity. Additionally, an intriguing finding was the translocation of live Probio-M9 from the gut to the mammary tissue only during bacterial mastitis and lactation, likely facilitated through lymphatic circulation. These findings advance our understanding of the intricate gut-mammary axis and provide valuable insights into the potential health benefits of probiotic interventions.},
}
@article {pmid39135692,
year = {2024},
author = {Wei, X and Guo, L and Cai, H and Gu, S and Tang, L and Leng, Y and Cheng, M and He, G and Han, Y and Ren, X and Lin, B and Lv, L and Shao, H and Wang, M and Wang, H and Dang, D and Wang, S and Wang, N and Shen, P and Wang, Q and Xu, Y and Jiang, Y and Zhang, N and He, X and Deng, X and Dai, M and Zhong, L and Xiong, Y and Pan, Y and Tang, K and Liu, F and Yang, B and Ren, L and Wang, J and Jiang, C and Huang, L},
title = {MASS cohort: Multicenter, longitudinal, and prospective study of the role of microbiome in severe pneumonia and host susceptibility.},
journal = {iMeta},
volume = {3},
number = {4},
pages = {e218},
pmid = {39135692},
issn = {2770-596X},
abstract = {The MASS cohort comprises 2000 ICU patients with severe pneumonia, covering community-acquired pneumonia, hospital-acquired pneumonia, and ventilator-associated pneumonia, sourced from 19 hospitals across 10 cities in three provinces. A wide array of samples including bronchoalveolar lavage fluid, sputum, feces, and whole blood are longitudinally collected throughout patients' ICU stays. The cohort study seeks to uncover the dynamics of lung and gut microbiomes and their associations with severe pneumonia and host susceptibility, integrating deep metagenomics and transcriptomics with detailed clinical data.},
}
@article {pmid39135686,
year = {2024},
author = {Geng, M and Li, M and Li, Y and Zhu, J and Sun, C and Wang, Y and Chen, WH},
title = {A universal oral microbiome-based signature for periodontitis.},
journal = {iMeta},
volume = {3},
number = {4},
pages = {e212},
pmid = {39135686},
issn = {2770-596X},
abstract = {We analyzed eight oral microbiota shotgun metagenomic sequencing cohorts from five countries and three continents, identifying 54 species biomarkers and 26 metabolic biomarkers consistently altered in health and disease states across three or more cohorts. Additionally, machine learning models based on taxonomic profiles achieved high accuracy in distinguishing periodontitis patients from controls (internal and external areas under the receiver operating characteristic curves of 0.86 and 0.85, respectively). These results support metagenome-based diagnosis of periodontitis and provide a foundation for further research and effective treatment strategies.},
}
@article {pmid39135685,
year = {2024},
author = {Ma, L and Lyu, W and Zeng, T and Wang, W and Chen, Q and Zhao, J and Zhang, G and Lu, L and Yang, H and Xiao, Y},
title = {Duck gut metagenome reveals the microbiome signatures linked to intestinal regional, temporal development, and rearing condition.},
journal = {iMeta},
volume = {3},
number = {4},
pages = {e198},
pmid = {39135685},
issn = {2770-596X},
abstract = {The duck gastrointestinal tract (GIT) harbors an abundance of microorganisms that play an important role in duck health and production. Here, we constructed the first relatively comprehensive duck gut microbial gene catalog (24 million genes) and 4437 metagenome-assembled genomes using 375 GIT metagenomic samples from four different duck breeds across five intestinal segments under two distinct rearing conditions. We further characterized the intestinal region-specific microbial taxonomy and their assigned functions, as well as the temporal development and maturation of the duck gut microbiome. Our metagenomic analysis revealed the similarity within the microbiota of the foregut and hindgut compartments, but distinctive taxonomic and functional differences between distinct intestinal segments. In addition, we found a significant shift in the microbiota composition of newly hatched ducks (3 days), followed by increased diversity and enhanced stability across growth stages (14, 42, and 70 days), indicating that the intestinal microbiota develops into a relatively mature and stable community as the host duck matures. Comparing the impact of different rearing conditions (with and without water) on duck cecal microbiota communities and functions, we found that the bacterial capacity for lipopolysaccharide biosynthesis was significantly increased in ducks that had free access to water, leading to the accumulation of pathogenic bacteria and antibiotic-resistance genes. Taken together, our findings expand the understanding of the microbiome signatures linked to intestinal regional, temporal development, and rearing conditions in ducks, which highlight the significant impact of microbiota on poultry health and production.},
}
@article {pmid39135636,
year = {2024},
author = {Cai, X and Sun, C and Zhong, H and Cai, Y and Cao, M and Wang, L and Sun, W and Tao, Y and Ma, G and Huang, B and Yan, S and Zhong, J and Wang, J and Lu, Y and Guan, Y and Song, M and Wang, Y and Li, Y and Su, X},
title = {The value of metagenomic next-generation sequencing with different nucleic acid extracting methods of cell-free DNA or whole-cell DNA in the diagnosis of non-neutropenic pulmonary aspergillosis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1398190},
pmid = {39135636},
issn = {2235-2988},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Bronchoalveolar Lavage Fluid/microbiology ; *Pulmonary Aspergillosis/diagnosis ; *Metagenomics/methods ; *Cell-Free Nucleic Acids ; Male ; Female ; *DNA, Fungal/genetics/isolation &amp; purification ; Middle Aged ; *ROC Curve ; Molecular Diagnostic Techniques/methods ; Aged ; Sensitivity and Specificity ; Adult ; },
abstract = {PURPOSE: Metagenomic next-generation sequencing(mNGS) is a novel molecular diagnostic technique. For nucleic acid extraction methods, both whole-cell DNA (wcDNA) and cell-free DNA (cfDNA) are widely applied with the sample of bronchoalveolar lavage fluid (BALF). We aim to evaluate the clinical value of mNGS with cfDNA and mNGS with wcDNA for the detection of BALF pathogens in non-neutropenic pulmonary aspergillosis.<br><br>METHODS: mNGS with BALF-cfDNA, BALF-wcDNA and conventional microbiological tests (CMTs) were performed in suspected non-neutropenic pulmonary aspergillosis. The diagnostic value of different assays for pulmonary aspergillosis was compared.<br><br>RESULTS: BALF-mNGS (cfDNA, wcDNA) outperformed CMTs in terms of microorganisms detection. Receiver operating characteristic (ROC) analysis indicated BALF-mNGS (cfDNA, wcDNA) was superior to culture and BALF-GM. Combination diagnosis of either positive for BALF-mNGS (cfDNA, wcDNA) or CMTs is more sensitive than CMTs alone in the diagnosis of pulmonary aspergillosis (BALF-cfDNA+CMTs/BALF-wcDNA+CMTs vs. CMTs: ROC analysis: 0.813 vs.0.66, P=0.0142/0.796 vs.0.66, P=0.0244; Sensitivity: 89.47% vs. 47.37%, P=0.008/84.21% vs. 47.37%, P=0.016). BALF-cfDNA showed a significantly greater reads per million (RPM) than BALF-wcDNA. The area under the ROC curve (AUC) for RPM of Aspergillus detected by BALF-cfDNA, used to predict "True positive" pulmonary aspergillosis patients, was 0.779, with a cut-off value greater than 4.5.<br><br>CONCLUSION: We propose that the incorporation of BALF-mNGS (cfDNA, wcDNA) with CMTs improves diagnostic precision in the identification of non-neutropenic pulmonary aspergillosis when compared to CMTs alone. BALF-cfDNA outperforms BALF-wcDNA in clinical value.},
}
@article {pmid39135559,
year = {2024},
author = {Song, Q and Li, Y and Zhou, T and Xiao, M and Xiao, B and Wang, M and Zhu, Y},
title = {Maternal vitamin D status during pregnancy and infant's gut microbiota: a prospective cohort study.},
journal = {Frontiers in nutrition},
volume = {11},
number = {},
pages = {1428356},
pmid = {39135559},
issn = {2296-861X},
abstract = {OBJECTIVES: To prospectively explore the association of maternal serum 25(OH)D levels with the infant's gut microbiota in Chinese populations, and to evaluate its potential influence on the dynamic change patterns of offspring's gut microbiota from 1 to 6 months old.<br><br>METHODS: Eighty-seven mother-infant dyads (vitamin D insufficient group vs. normal group&#x2009;=&#x2009;59 vs. 28) were included in this longitudinal study. Two fecal samples were collected for the included infant at home by the parents at 1&#x2009;month of age ("M1 phase") and 6&#x2009;months of age ("M6 phase"). Gut microbiota were profiled by 16S rRNA gene sequencing. We performed mixed effects models on alpha diversity metrics, PERMANOVA tests on beta diversity distances, and linear discriminant analysis (LDA) to identify differently abundant taxa.<br><br>RESULTS: We observed significantly lower Pielou's evenness and Shannon diversity in the vitamin D insufficient group in the M6 phase (p&#x2009;=&#x2009;0.049 and 0.015, respectively), but not in the M1 phase (p&#x2009;>&#x2009;0.05), and the dynamic changes in alpha diversity from 1 to 6&#x2009;months old were significantly different according to maternal vitamin D status (p&#x2009;<&#x2009;0.05). There were also significant differences in gut microbiota composition between the vitamin D insufficient group and normal group, both in the M1 and M6 phases (LDA score&#x2009;>&#x2009;2.0, p&#x2009;<&#x2009;0.05). Moreover, among the predicted metagenome functions, pathways related to amino acid biosynthesis, starch degradation, and purine nucleotides biosynthesis were enriched in the vitamin D insufficient group.<br><br>CONCLUSION: Our findings highlight that maternal vitamin D status plays a pivotal role in shaping the early-life gut microbiota of the next generation.},
}
@article {pmid39134956,
year = {2024},
author = {Liu, D and Li, N and Zhu, Y and Chen, Q and Fan, X and Feng, J},
title = {Diagnosis of human angiostrongyliasis in a case of hydrocephalus using next-generation sequencing: a case report and literature review.},
journal = {BMC neurology},
volume = {24},
number = {1},
pages = {281},
pmid = {39134956},
issn = {1471-2377},
mesh = {Humans ; *Strongylida Infections/diagnosis/drug therapy/complications ; Male ; *Angiostrongylus cantonensis/genetics/isolation &amp; purification ; *High-Throughput Nucleotide Sequencing/methods ; Adolescent ; Animals ; *Hydrocephalus/diagnosis/parasitology ; },
abstract = {BACKGROUND: Angiostrongyliasis cantonensis is a severe yet rare parasitic infection caused by the larvae of Angiostrongylus cantonensis. The primary characteristic feature of this foodborne illness in humans is eosinophilic meningitis. Recently, there has been a gradual increase in reported cases globally. Due to the lack of typical clinical symptoms, signs, and specific laboratory tests, early diagnosis of this disease poses significant challenges. Failure to diagnose and treat this condition promptly can result in fatalities.<br><br>METHODS: We present the case of a 13-year-old male patient who initially presented with fever and headache. The patient was preliminarily diagnosed with bacterial meningitis and received treatment with antibacterial drugs. However, the patient's condition worsened, and he developed progressive consciousness disturbances. Eventually, metagenomic next-generation sequencing (mNGS) testing of cerebrospinal fluid samples indicated Angiostrongylus cantonensis infection. Following treatment with albendazole and prednisone, the patient made a full recovery. We include this case report as part of a literature review to emphasize the potential applications of mNGS in the early diagnosis of Angiostrongyliasis cantonensis.<br><br>CONCLUSION: mNGS technology plays a crucial role in the diagnosis of angiostrongyliasis cantonensis. As this technology continues to evolve and be applied, we believe it will play an increasingly important role in diagnosing, treating, and monitoring angiostrongyliasis cantonensis.},
}
@article {pmid39134651,
year = {2024},
author = {Gutiérrez-Preciado, A and Dede, B and Baker, BA and Eme, L and Moreira, D and López-García, P},
title = {Extremely acidic proteomes and metabolic flexibility in bacteria and highly diversified archaea thriving in geothermal chaotropic brines.},
journal = {Nature ecology &amp; evolution},
volume = {},
number = {},
pages = {},
pmid = {39134651},
issn = {2397-334X},
support = {doi.org/10.37807/GBMF9739//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 787904//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; },
abstract = {Few described archaeal, and fewer bacterial, lineages thrive under salt-saturating conditions, such as solar saltern crystallizers (salinity above 30% w/v). They accumulate molar K[+] cytoplasmic concentrations to maintain osmotic balance ('salt-in' strategy) and have proteins adaptively enriched in negatively charged acidic amino acids. Here we analysed metagenomes and metagenome-assembled genomes from geothermally influenced hypersaline ecosystems with increasing chaotropicity in the Danakil Depression. Normalized abundances of universal single-copy genes confirmed that haloarchaea and Nanohaloarchaeota encompass 99% of microbial communities in the near-life-limiting conditions of the Western-Canyon Lakes. Danakil metagenome- and metagenome-assembled-genome-inferred proteomes, compared with those of freshwater, seawater and solar saltern ponds up to saturation (6-14-32% salinity), showed that Western-Canyon Lake archaea encode the most acidic proteomes ever observed (median protein isoelectric points ≤4.4). We identified previously undescribed haloarchaeal families as well as an Aenigmatarchaeota family and a bacterial phylum independently adapted to extreme halophily. Despite phylum-level diversity decreasing with increasing salinity-chaotropicity, and unlike in solar salterns, adapted archaea exceedingly diversified in Danakil ecosystems, challenging the notion of decreasing diversity under extreme conditions. Metabolic flexibility to utilize multiple energy and carbon resources generated by local hydrothermalism along feast-and-famine strategies seemingly shapes microbial diversity in these ecosystems near life limits.},
}
@article {pmid39134606,
year = {2024},
author = {Austin, RM and Honap, TP and Mann, AE and Hübner, A and DeGaglia, CMS and Warinner, C and Zuckerman, MK and Hofman, CA},
title = {Publisher Correction: Metagenomic and paleopathological analyses of a historic documented collection explore ancient dental calculus as a diagnostic tool.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {18723},
doi = {10.1038/s41598-024-69609-8},
pmid = {39134606},
issn = {2045-2322},
}
@article {pmid39134593,
year = {2024},
author = {Trosvik, P and Noordzij, HT and de Muinck, EJ},
title = {Antibiotic resistance gene dynamics in the commensal infant gut microbiome over the first year of life.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {18701},
pmid = {39134593},
issn = {2045-2322},
support = {300948//Norges Forskningsr&#xe5;d/ ; },
mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; Infant ; *Feces/microbiology ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Metagenomics/methods ; Metagenome ; Genes, Bacterial ; Bacteria/genetics/classification ; Infant, Newborn ; Female ; },
abstract = {Colonization of the infant gut is an important developmental process characterized by high carriage of antimicrobial resistance genes (ARGs) and high abundances of pathobionts. The horizontal transfer of ARGs to pathogenic bacteria represents a major public health concern. However, there is still a paucity of longitudinal studies surveilling ARGs in healthy infant guts at high temporal resolution. Furthermore, we do not yet have a clear view of how temporal variation in ARG carriage relates to the dynamics of specific bacterial populations, as well as community virulence potential. Here, we performed deep shotgun metagenomic sequencing of monthly fecal samples from a cohort of 12 infants, covering the first year of life to interrogate the infant gut microbiome for ARG content. We further relate ARG dynamics to the dynamics of taxa, virulence potential, as well as the potential for ARG mobilization. We identify a core resistome dominated by efflux systems typically associated with Enterobacteriaceae. Overall ARG carriage declined over the first year of life and showed strong contemporaneous correlation with the population dynamics of Proteobacteria. Furthermore, the majority of ARGs could be further mapped to metagenome-assembled genomes (MAGs) classified to this phylum. We were able to assign a large number of ARGs to E. coli by correlating the temporal dynamics of individual genes with species dynamics, and we show that the temporal dynamics of ARGs and virulence factors are highly correlated, suggesting close taxonomic associations between these two gene classes. Finally, we identify ARGs linked with various categories of mobile genetic elements, demonstrating preferential linkage among mobility categories and resistance to different drug classes. While individual variation in ARG carriage is substantial during infancy there is a clear reduction over the first year of life. With few exceptions, ARG abundances closely track the dynamics of pathobionts and community virulence potential. These findings emphasize the potential for development of resistant pathogens in the developing infant gut, and the importance of effective surveillance in order to detect such events.},
}
@article {pmid39133581,
year = {2024},
author = {Attaway, C and Mathison, BA and Misra, A},
title = {No longer stuck in the past: new advances in artificial intelligence and molecular assays for parasitology screening and diagnosis.},
journal = {Current opinion in infectious diseases},
volume = {37},
number = {5},
pages = {357-366},
pmid = {39133581},
issn = {1473-6527},
mesh = {*Artificial Intelligence ; Humans ; *Parasitic Diseases/diagnosis ; Molecular Diagnostic Techniques/methods ; Parasitology/methods ; Sensitivity and Specificity ; },
abstract = {PURPOSE OF REVIEW: Emerging technologies are revolutionizing parasitology diagnostics and challenging traditional methods reliant on microscopic analysis or serological confirmation, which are known for their limitations in sensitivity and specificity. This article sheds light on the transformative potential of artificial intelligence and molecular assays in the field, promising more accurate and efficient detection methods.<br><br>RECENT FINDINGS: Artificial intelligence has emerged as a promising tool for blood and stool parasite review, when paired with comprehensive databases and expert oversight result in heightened specificity and sensitivity of diagnoses while also increasing efficiency. Significant strides have been made in nucleic acid testing for multiplex panels for enteric pathogen. Both multiplex and single target panels for Plasmodium , Babesia , filaria, and kinetoplastids have been developed and garnered regulatory approval, notably for blood donor screening in the United States. Additional technologies such as MALDI-TOF, metagenomics, flow cytometry, and CRISPR-Cas are under investigation for their diagnostic utility and are currently in the preliminary stages of research and feasibility assessment.<br><br>SUMMARY: Recent implementation of artificial intelligence and digital microscopy has enabled swift smear screening and diagnosis, although widespread implementation remains limited. Simultaneously, molecular assays - both targeted and multiplex panels are promising and have demonstrated promise in numerous studies with some assays securing regulatory approval recently. Additional technologies are under investigation for their diagnostic utility and are compelling avenues for future proof-of-concept diagnostics.},
}
@article {pmid39133323,
year = {2024},
author = {Nehra, C and Harshini, V and Shukla, N and Chavda, P and Savaliya, K and Patil, S and Shah, T and Pandit, R and Patil, NV and Patel, AK and Kachhawaha, S and Kumawat, RN and Joshi, M and Joshi, CG},
title = {Moringa leaf meal exerts growth benefits in small ruminants through modulating the gastrointestinal microbiome.},
journal = {Applied microbiology and biotechnology},
volume = {108},
number = {1},
pages = {438},
pmid = {39133323},
issn = {1432-0614},
support = {Project Reference No: BT/AQ/1/SP41105/2020//Department of Biotechnology, Ministry of Science and Technology, India/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Animal Feed/analysis ; *Plant Leaves ; *Moringa/chemistry ; Sheep ; *Feces/microbiology ; *Goats ; Dietary Supplements ; Fatty Acids, Volatile/metabolism ; Rumen/microbiology ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Weight Gain/drug effects ; Diet/veterinary ; Metagenomics ; },
abstract = {This study investigated the impact of feeding 17% moringa leaf meal (MLM) on the ruminal and fecal microbial composition and body weight gain (BWG) performance of lambs (Ovis aries) and kids (Capra hircus). A total of n = 28 lambs (n = 14, no-moringa, n = 14, 17% moringa) and 24 kids (n = 12, no-moringa, n = 12, 17% moringa) were involved in the experiment and body weight was recorded fortnightly. Metagenomic shotgun sequencing was performed on 28, 22, and 26 ruminal solid, liquid fraction, and fecal samples from lambs, and 23, 22, and 23 samples from kids. Moringa supplementation significantly increased BWG in lambs (21.09 ± 0.78 to 26.12 ± 0.81 kg) and kids (14.60 ± 1.29 to 18.28 ± 1.09 kg) (p-value ≤ 0.01). Microbiome analysis revealed an elevated Firmicutes:Bacteroidetes ratio in the moringa diet group. Moringa-fed animals exhibited increased microbial genera associated with volatile fatty acids (VFAs) production (Prevotella, Anaerovibrio, Lachnospiraceae, Butyrivibrio, Christensenella) and starch and fiber digesters (Proteobacteria, Ruminococcus). The increase in the bacterial genus Sharpea suggested possible methane reduction and decreased proportion of pathogens, Aliarcobacter_ID28198, Campylobacter_ID194 and Campylobacter_ID1660076 suggest health benefits. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis demonstrated significant alterations in microbial gene pool and metabolic pathways related to carbohydrate, protein, lipid and energy metabolism, indicating potential improvements in animal health. Overall, moringa feeding showed higher energy recovery, improved growth, and potential benefits in methane reduction and reduced pathogenic bacteria.},
}
@article {pmid39133000,
year = {2024},
author = {Tothero, GK and Hoover, RL and Farag, IF and Kaplan, DI and Weisenhorn, P and Emerson, D and Chan, CS},
title = {Leptothrix ochracea genomes reveal potential for mixotrophic growth on Fe(II) and organic carbon.},
journal = {Applied and environmental microbiology},
volume = {90},
number = {9},
pages = {e0059924},
pmid = {39133000},
issn = {1098-5336},
support = {P20GM103446//HHS | National Institutes of Health (NIH)/ ; EAR-2243577//National Science Foundation (NSF)/ ; DE-AC02-06CH11357//U.S. Department of Energy (DOE)/ ; OIA-1826734//National Science Foundation (NSF)/ ; P20 GM103446/GM/NIGMS NIH HHS/United States ; DE-SC0021010//U.S. Department of Energy (DOE)/ ; DE-EM0005228//U.S. Department of Energy (DOE)/ ; EAR-1833525//National Science Foundation/ ; },
mesh = {*Carbon/metabolism ; *Genome, Bacterial ; *Leptothrix/metabolism/genetics/growth &amp; development ; Wetlands ; Ferrous Compounds/metabolism ; Oxidation-Reduction ; Iron/metabolism ; Carbon Cycle ; Autotrophic Processes ; Metagenome ; },
abstract = {UNLABELLED: Leptothrix ochracea creates distinctive iron-mineralized mats that carpet streams and wetlands. Easily recognized by its iron-mineralized sheaths, L. ochracea was one of the first microorganisms described in the 1800s. Yet it has never been isolated and does not have a complete genome sequence available, so key questions about its physiology remain unresolved. It is debated whether iron oxidation can be used for energy or growth and if L. ochracea is an autotroph, heterotroph, or mixotroph. To address these issues, we sampled L. ochracea-rich mats from three of its typical environments (a stream, wetlands, and a drainage channel) and reconstructed nine high-quality genomes of L. ochracea from metagenomes. These genomes contain iron oxidase genes cyc2 and mtoA, showing that L. ochracea has the potential to conserve energy from iron oxidation. Sox genes confer potential to oxidize sulfur for energy. There are genes for both carbon fixation (RuBisCO) and utilization of sugars and organic acids (acetate, lactate, and formate). In silico stoichiometric metabolic models further demonstrated the potential for growth using sugars and organic acids. Metatranscriptomes showed a high expression of genes for iron oxidation; aerobic respiration; and utilization of lactate, acetate, and sugars, as well as RuBisCO, supporting mixotrophic growth in the environment. In summary, our results suggest that L. ochracea has substantial metabolic flexibility. It is adapted to iron-rich, organic carbon-containing wetland niches, where it can thrive as a mixotrophic iron oxidizer by utilizing both iron oxidation and organics for energy generation and both inorganic and organic carbon for cell and sheath production.<br><br>IMPORTANCE: Winogradsky's observations of L. ochracea led him to propose autotrophic iron oxidation as a new microbial metabolism, following his work on autotrophic sulfur-oxidizers. While much culture-based research has ensued, isolation proved elusive, so most work on L. ochracea has been based in the environment and in microcosms. Meanwhile, the autotrophic Gallionella became the model for freshwater microbial iron oxidation, while heterotrophic and mixotrophic iron oxidation is not well-studied. Ecological studies have shown that Leptothrix overtakes Gallionella when dissolved organic carbon content increases, demonstrating distinct niches. This study presents the first near-complete genomes of L. ochracea, which share some features with autotrophic iron oxidizers, while also incorporating heterotrophic metabolisms. These genome, metabolic modeling, and transcriptome results give us a detailed metabolic picture of how the organism may combine lithoautotrophy with organoheterotrophy to promote Fe oxidation and C cycling and drive many biogeochemical processes resulting from microbial growth and iron oxyhydroxide formation in wetlands.},
}
@article {pmid39132143,
year = {2024},
author = {Zhao, Z and Zhao, Y and Marotta, F and Xamxidin, M and Li, H and Xu, J and Hu, B and Wu, M},
title = {The microbial community structure and nitrogen cycle of high-altitude pristine saline lakes on the Qinghai-Tibetan plateau.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1424368},
pmid = {39132143},
issn = {1664-302X},
abstract = {The nitrogen (N) cycle is the foundation of the biogeochemistry on Earth and plays a crucial role in global climate stability. It is one of the most important nutrient cycles in high-altitude lakes. The biogeochemistry of nitrogen is almost entirely dependent on redox reactions mediated by microorganisms. However, the nitrogen cycling of microbial communities in the high-altitude saline lakes of the Qinghai-Tibet Plateau (QTP), the world's "third pole" has not been investigated extensively. In this study, we used a metagenomic approach to investigate the microbial communities in four high-altitude pristine saline lakes in the Altun mountain on the QTP. We observed that Proteobacteria, Bacteroidota, and Actinobacteriota were dominant in these lakes. We reconstructed 1,593 bacterial MAGs and 8 archaeal MAGs, 1,060 of which were found to contain nitrogen cycle related genes. Our analysis revealed that nitrite reduction, nitrogen fixation, and assimilatory nitrate reduction processes might be active in the lakes. Denitrification might be a major mechanism driving the potential nitrogen loss, while nitrification might be inactive. A wide variety of microorganisms in the lake, dominated by Proteobacteria, participate together in the nitrogen cycle. The prevalence of the dominant taxon Yoonia in these lakes may be attributed to its well-established nitrogen functions and the coupled proton dynamics. This study is the first to systematically investigate the structure and nitrogen function of the microbial community in the high-altitude pristine saline lakes in the Altun mountain on the QTP. As such, it contributes to a better comprehension of biogeochemistry of high-altitude saline lakes.},
}
@article {pmid39132136,
year = {2024},
author = {Sun, Y and Wang, Y and Ji, L and Zhao, Q and Shen, Q and Wang, X and Liu, Y and Ji, L and Yang, S and Zhang, W},
title = {Identification and characterization of multiple novel picornaviruses in fecal samples of bar-headed goose.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1440801},
pmid = {39132136},
issn = {1664-302X},
abstract = {INTRODUCTION: The bar-headed goose (Anser indicus), one of the most well-known high-altitude birds, is renowned for its adaptation to high-altitude environments. Previous studies have shown that they can be infected with highly pathogenic avian influenza; however, there is currently limited research on other viruses in bar-headed geese.<br><br>METHODS: In this study, 10 fecal samples of healthy bar-headed geese were collected, and viral metagenomics method was conducted to identify novel picornaviruses.<br><br>RESULTS: Seven novel picornaviruses were identified in the fecal samples of bar-headed geese. Most of these picornaviruses were genetically different from other currently known viruses in the NCBI dataset. Among them, PICV4 was determined to be a new species belonging to the Anativirus genus, PICV5 and PICV13 were classified as novel species belonging to the Hepatovirus genus, and the remaining four picornaviruses (PICV1, PICV19, PICV21, and PICV22) were identified as part of the Megrivirus A species of the Megrivirus genus. Recombinant analysis indicates that PICV21 was a potential recombinant, and the major and minor parents were PICV1 and PICV22, respectively.<br><br>CONCLUSION: The findings of this study increase our understanding of the diversity of picornaviruses in bar-headed geese and provide practical viral genome information for the prevention and treatment of potential viral diseases affecting this species.},
}
@article {pmid39132133,
year = {2024},
author = {Ayaz, M and Zhao, JT and Zhao, W and Chi, YK and Ali, Q and Ali, F and Khan, AR and Yu, Q and Yu, JW and Wu, WC and Qi, RD and Huang, WK},
title = {Biocontrol of plant parasitic nematodes by bacteria and fungi: a multi-omics approach for the exploration of novel nematicides in sustainable agriculture.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1433716},
pmid = {39132133},
issn = {1664-302X},
abstract = {Plant parasitic nematodes (PPNs) pose a significant threat to global crop productivity, causing an estimated annual loss of US $157 billion in the agriculture industry. While synthetic chemical nematicides can effectively control PPNs, their overuse has detrimental effects on human health and the environment. Biocontrol agents (BCAs), such as bacteria and fungi in the rhizosphere, are safe and promising alternatives for PPNs control. These BCAs interact with plant roots and produce extracellular enzymes, secondary metabolites, toxins, and volatile organic compounds (VOCs) to suppress nematodes. Plant root exudates also play a crucial role in attracting beneficial microbes toward infested roots. The complex interaction between plants and microbes in the rhizosphere against PPNs is mostly untapped which opens new avenues for discovering novel nematicides through multi-omics techniques. Advanced omics approaches, including metagenomics, transcriptomics, proteomics, and metabolomics, have led to the discovery of nematicidal compounds. This review summarizes the status of bacterial and fungal biocontrol strategies and their mechanisms for PPNs control. The importance of omics-based approaches for the exploration of novel nematicides and future directions in the biocontrol of PPNs are also addressed. The review highlighted the potential significance of multi-omics techniques in biocontrol of PPNs to ensure sustainable agriculture.},
}
@article {pmid39131798,
year = {2024},
author = {Liu, W and Li, C and Xie, W and Fan, Y and Zhang, X and Wang, Y and Li, L and Zhang, Z},
title = {The signature of the gut microbiota associated with psoriatic arthritis revealed by metagenomics.},
journal = {Therapeutic advances in musculoskeletal disease},
volume = {16},
number = {},
pages = {1759720X241266720},
pmid = {39131798},
issn = {1759-720X},
abstract = {BACKGROUND: Gut microbiota is involved in the development of psoriatic arthritis (PsA), but until now, there has been a lack of understanding of the PsA host-bacteria interaction.<br><br>OBJECTIVES: To reveal the labels of gut microbiota in PsA patients and the species and functions related to disease activity.<br><br>DESIGN: Observational research (cross-sectional) with an exploratory nature.<br><br>METHODS: Metagenomics sequencing was used to analyze stool samples from 20 treatment-na&#xef;ve PsA patients and 10 age-matched healthy individuals. All samples were qualified for subsequent analysis.<br><br>RESULTS: Compared with the healthy group, &#x3b1;-diversity was reduced in the PsA group, and &#x3b2;-diversity could distinguish the two groups. Two bacteria with high abundance and correlation with PsA disease activity were identified, Bacteroides sp. 3_1_19 and Blautia AF 14-40. In different functions, K07114 (calcium-activated chloride channel (CaCC) homolog) showed a positive correlation with PsA disease activity (disease activity in psoriatic arthritis, DAPSA) and Tet32 (an antibiotic-resistant gene), and carbohydrate-binding module family 50 was negatively correlated with erythrocyte sedimentation rate. A bacterial co-expression network associated with DAPSA was constructed. The network was centered on the bacteria in the Bacteroides genus, which formed a closely related network and were positively correlated with DAPSA. As another core of the network, K07114 was closely related to multiple bacteria in the Bacteroides genus and is also positively correlated with disease activity.<br><br>CONCLUSION: The network composed of Bacteroides is associated with PsA disease activity, and its therapeutic value needs to be further explored. CaCCs may be a key channel for the interaction between Bacteroides and PsA-host.},
}
@article {pmid39131619,
year = {2024},
author = {Kahsen, J and Sherwani, SK and Naqib, A and Jeon, T and Wu, LYA and Green, SJ},
title = {Quantitating primer-template interactions using deconstructed PCR.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e17787},
pmid = {39131619},
issn = {2167-8359},
mesh = {*Polymerase Chain Reaction/methods ; *DNA Primers/genetics ; Templates, Genetic ; Metagenomics/methods ; DNA/genetics ; },
abstract = {When the polymerase chain reaction (PCR) is used to amplify complex templates such as metagenomic DNA using single or degenerate primers, preferential amplification of templates (PCR bias) leads to a distorted representation of the original templates in the final amplicon pool. This bias can be influenced by mismatches between primers and templates, the locations of mismatches, and the nucleotide pairing of mismatches. Many studies have examined primer-template interactions through interrogation of the final products of PCR amplification with controlled input templates. Direct measurement of primer-template interactions, however, has not been possible, leading to uncertainty when optimizing PCR reactions and degenerate primer pools. In this study, we employed a method developed to reduce PCR bias (i.e., Deconstructed PCR, or DePCR) that also provides empirical data regarding primer-template interactions during the first two cycles of PCR amplification. We systematically examined interactions between primers and templates using synthetic DNA templates and varying primer pools, amplified using standard PCR and DePCR protocols. We observed that in simple primer-template systems, perfect match primer-template interactions are favored, particularly when mismatches are close to the 3' end of the primer. In more complex primer-template systems that better represent natural samples, mismatch amplifications can dominate, and heavily degenerate primer pools can improve representation of input templates. When employing the DePCR methodology, mismatched primer-template annealing led to amplification of source templates with significantly lower distortion relative to standard PCR. We establish here a quantitative experimental system for interrogating primer-template interactions and demonstrate the efficacy of DePCR for amplification of complex template mixtures with complex primer pools.},
}
@article {pmid39131363,
year = {2024},
author = {Martin, C and Gitter, A and Anantharaman, K},
title = {Protein Set Transformer: A protein-based genome language model to power high diversity viromics.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39131363},
issn = {2692-8205},
support = {R35 GM143024/GM/NIGMS NIH HHS/United States ; },
abstract = {Exponential increases in microbial and viral genomic data demand transformational advances in scalable, generalizable frameworks for their interpretation. Standard homology-based functional analyses are hindered by the rapid divergence of microbial and especially viral genomes and proteins that significantly decreases the volume of usable data. Here, we present Protein Set Transformer (PST), a protein-based genome language model that models genomes as sets of proteins without considering sparsely available functional labels. Trained on >100k viruses, PST outperformed other homology- and language model-based approaches for relating viral genomes based on shared protein content. Further, PST demonstrated protein structural and functional awareness by clustering capsid-fold-containing proteins with known capsid proteins and uniquely clustering late gene proteins within related viruses. Our data establish PST as a valuable method for diverse viral genomics, ecology, and evolutionary applications. We posit that the PST framework can be a foundation model for microbial genomics when trained on suitable data.},
}
@article {pmid39131354,
year = {2024},
author = {Özcan, E and Yu, KB and Dinh, L and Lum, GR and Lau, K and Hsu, J and Arino, M and Paramo, J and Lopez-Romero, A and Hsiao, EY},
title = {Dietary fiber content in clinical ketogenic diets modifies the gut microbiome and seizure resistance in mice.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39131354},
issn = {2692-8205},
support = {R01 NS115537/NS/NINDS NIH HHS/United States ; },
abstract = {The gut microbiome is emerging as an important modulator of the anti-seizure effects of the classic ketogenic diet. However, many variations of the ketogenic diet are used clinically to treat refractory epilepsy, and how different dietary formulations differentially modify the gut microbiome in ways that impact seizure outcome is poorly understood. We find that clinically prescribed ketogenic infant formulas vary in macronutrient ratio, fat source, and fiber content and also in their ability to promote resistance to 6-Hz psychomotor seizures in mice. By screening specific dietary variables for their effects on a model human infant microbial community, we observe that dietary fiber, rather than fat ratio or source, drives substantial metagenomic shifts. Addition of dietary fiber to a fiber-deficient ketogenic formula restores seizure resistance, and supplementing protective ketogenic formulas with excess dietary fiber further potentiates seizure resistance. By screening 13 fiber sources and types, we identify distinct subsets of metagenomic responses in the model human infant microbial community that correspond with increased seizure resistance in mice. In particular, supplementation with seizure-protective fibers enriches microbial representation of genes related to queuosine biosynthesis and preQ0 biosynthesis and decreases representation of microbial genes related to sucrose degradation, which is also seen in seizure-protected mice that are fed fiber-containing ketogenic infant formulas. Overall, this study reveals that different formulations of clinical ketogenic diets, and dietary fiber content in particular, differentially impact seizure outcome in mice, likely through modification of the gut microbiome. Understanding interactions between dietary components of the ketogenic diet, the gut microbiome, and host susceptibility to seizures could inform novel microbiome-guided approaches to treat refractory epilepsy.},
}
@article {pmid39130737,
year = {2024},
author = {Hinds, J and Apaa, T and Parry, RH and Withers, AJ and MacKenzie, L and Staley, C and Morrison, J and Bennett, M and Bremner-Harrison, S and Chadwick, EA and Hailer, F and Harrison, SWR and Lambin, X and Loose, M and Mathews, F and Tarlinton, R and Blanchard, A},
title = {Multiple novel caliciviruses identified from stoats (Mustela erminea) in the United Kingdom.},
journal = {Access microbiology},
volume = {6},
number = {7},
pages = {},
pmid = {39130737},
issn = {2516-8290},
abstract = {The Caliciviridae family, comprising positive-sense RNA viruses, is characterised by its non-enveloped, small virions, broad host range, and notable tendency for host switching. These viruses are primarily associated with gastroenteric disease, though they can lead to haemorrhagic or respiratory infections. Our study employed a metagenomics analysis of faecal samples from stoats (Mustela erminea), identifying two novel calicivirus species, named stoat vesivirus and stoat valovirus. Stoat vesivirus was identified in three samples (ST008, ST006, ST004), exhibiting a genome wide nucleotide identity of approximately 92 %. The complete coding sequences of these samples were 8471 (ST004) and 8322 (ST006) nucleotides in length, respectively. Each comprised three open reading frames (ORF), closely resembling the Vesivirus mink calicivirus (China/2/2016), with 70-72 % similarity in ORF1, 61-62 % in ORF2 and 71 % in ORF3. Phylogenetic analysis robustly supported stoat vesivirus as belonging within the Vesivirus genus. The second calivicirus (stoat valovirus), detected solely in sample ST008, was 6527 nucleotides in length and with complete coding sequences present. It shared highest similarity with St-Valérien swine virus and marmot norovirus HT16, showing 39.5 and 38.8 % protein identity with ORF1 and 43.3 and 42.9 % for VP1. Stoat valovirus is borderline for meeting the ICTV criteria for a new genus, demonstrating 60 % divergence in ORF1 compared to the other valovirus', however it clusters basally within the Valovirus genus, supporting leaving it included in this genus.},
}
@article {pmid39130570,
year = {2024},
author = {Gao, Y and Wang, W and Jiang, S and Jin, Z and Guo, M and Wang, M and Li, H and Cui, K},
title = {Response Characteristics of the Community Structure and Metabolic Genes of Oil-Recovery Bacteria after Targeted Activation of Petroleum Hydrocarbon-Degrading Bacteria in Low-Permeability Oil Reservoirs.},
journal = {ACS omega},
volume = {9},
number = {31},
pages = {33448-33458},
pmid = {39130570},
issn = {2470-1343},
abstract = {The microbial enhanced oil recovery (MEOR) process has been identified as a promising alternative to conventional enhanced oil recovery methods because it is eco-friendly and economically advantageous. However, the knowledge about the composition and diversity of microbial communities in artificially regulated reservoirs, especially after activating petroleum hydrocarbon-degrading bacteria (PHDB) by injecting exogenous nutrients, is still insufficient. This study utilized a combination of high-throughput sequencing and metagenomics technology to reveal the structural evolution characteristics of the indigenous microbial community in the reservoir during the PHDB activated for enhanced oil recovery, as well as the response relationship between the expression of its oil production functional genes and crude oil biodegradation. Results showed that Pseudomonas (>75%) gradually evolves into a stable dominant microbial community in the reservoir during the activation of PHDB. Besides, the gene expression and KEGG pathways after crude oil undergoes biodegradation by PHDB show that the number of genes related to petroleum hydrocarbon metabolism dominates the metabolism (21.98%). Meanwhile, a preliminary schematic diagram was drawn to illustrate the evolution mechanism of the EOR metabolic pathway after the targeted activation of PHDB. Additionally, it was found that the abundance of hydrocarbon-degrading enzymes increased significantly, and the activity of alcohol dehydrogenase was higher than that of aldehyde dehydrogenase and monooxygenase after PHDB activation. These research results not only filled in and expanded the theoretical knowledge of MEOR based on artificial interference or regulation of reservoir oil-recovery functional microbial community structure but also provided guidance for the future application of MEOR technology in oil field operations.},
}
@article {pmid39130256,
year = {2024},
author = {Kanodia, A and Monga, R and Ilyas, M and Verma, Y and Mohapatra, S and Rao, NS and Vyas, M and Sikka, K and Atmakuri, K},
title = {Metagenome Analysis of Cholesteatoma-associated Bacteria: A Pilot Study.},
journal = {Indian journal of otolaryngology and head and neck surgery : official publication of the Association of Otolaryngologists of India},
volume = {76},
number = {4},
pages = {3307-3318},
pmid = {39130256},
issn = {2231-3796},
abstract = {INTRODUCTION: Cholesteatoma usually harbors a poly-microbial infection. As the diversity of bacterial pathogens in the Indian COM is unknown, we set out to identify the bacteria associated with cholesteatoma disease in different patients of North India using targeted metagenomic analysis of the 16 S rRNA gene.<br><br>METHODS: We recruited 15 patients of cholesteatomatous chronic otitis media (COM), who underwent surgical disease clearance. We divided these patients into four groups based on the four clinic-radiological stages categorized as per the EAONO/JOS joint consensus statement classification. Representative samples were extracted during the surgery and sent for bacterial culture and sensitivity and 16&#xa0;S rRNA gene metagenomic analysis.<br><br>RESULTS: While 12 (80%) of the patients belonged to clinical Stage I/II; one patient had an extracranial complication (stage III) and two patients had an intracranial complication (stage IV). Our detailed bacterial metagenomics analyses showed that while phylum Proteobacteria was most abundant (reads up to &#x223c;&#x2009;95%) in specimens from nine patients, phylum Firmicutes was most abundant (up to &#x223c;&#x2009;80%) in specimens from four patients. Gamma (&#x3b3;) Proteobacteria and Epsilon (&#x3b5;) Proteobacteria were the most abundant class amongst Proteobacteria. Class Tissierellia stood out as the most abundant Firmicutes (40-60%), followed by Clostridia (20%) and Bacilli (10%). There was negligible difference in the bacterial profiles across all four clinical stages.<br><br>CONCLUSION: Cholesteatoma is primarily associated with Proteobacteria and Firmicutes phyla, even in complicated disease. Further studies with a larger sample size are required to validate our findings.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12070-024-04678-9.},
}
@article {pmid39129952,
year = {2024},
author = {Golob, J and Rao, K and Berinstein, JA and Chey, WD and Owyang, C and Kamada, N and Higgins, PDR and Young, V and Bishu, S and Lee, AA},
title = {The Microbiome in Quiescent Crohn's Disease With Persistent Symptoms Show Disruptions in Microbial Sulfur and Tryptophan Pathways.},
journal = {Gastro hep advances},
volume = {3},
number = {2},
pages = {167-177},
pmid = {39129952},
issn = {2772-5723},
abstract = {BACKGROUND AND AIMS: Even in the absence of inflammation, persistent symptoms in Crohn's disease (CD) are prevalent and worsen quality of life. Amongst patients without inflammation (quiescent CD), we hypothesized that microbial community structure and function, including tryptophan metabolism, would differ between patients with persistent symptoms (qCD + S) and without persistent symptoms (qCD-S).<br><br>METHODS: We performed a multicenter observational study nested within the Study of a Prospective Adult Research Cohort with Inflammatory Bowel Disease. Quiescent inflammation was defined by fecal calprotectin level <150 mcg/g. Persistent symptoms were defined by Crohn's Disease Patient-Reported Outcome-2. Active CD, diarrhea-predominant irritable bowel syndrome, and healthy controls were included as controls. Stool samples underwent whole-genome shotgun metagenomic sequencing.<br><br>RESULTS: Thirty-nine patients with qCD&#xa0;+ S, 274 qCD-S, 21 active CD, 40 diarrhea-predominant irritable bowel syndrome, and 50 healthy controls were included for analysis. Patients with qCD&#xa0;+ S had a less-diverse microbiome. Furthermore, patients with qCD&#xa0;+ S showed significant enrichment of bacterial species that are normal inhabitants of the oral microbiome (eg Rothia dentocariosa, Fusobacterium nucleatum) and sulfidogenic microbes (eg Prevotella copri, Bilophila spp.). Depletion of important butyrate and indole producers (eg Eubacterium rectale, Faecalibacterium prausnitzii) was also noted in qCD&#xa0;+ S. Potential metagenome-related functional changes in cysteine and methionine metabolism, ATP transport, and redox reactions were disturbed in qCD&#xa0;+ S, also suggestive of altered sulfur metabolism. Finally, qCD&#xa0;+ S showed significant reductions in bacterial tnaA genes, which mediate tryptophan metabolism to indole, and significant tnaA allelic variation compared with qCD-S.<br><br>CONCLUSION: The microbiome in qCD&#xa0;+ S showed significant differences in sulfidogenesis, butyrate producers, and typically oral microbes compared to qCD-S and active CD. These results suggest that inflammation may lead to durable microbiome alterations which may mediate persistent symptoms through testable mechanisms.},
}
@article {pmid39129834,
year = {2024},
author = {Sabsay, KR and Te Velthuis, AJW},
title = {Using structure prediction of negative sense RNA virus nucleoproteins to assess evolutionary relationships.},
journal = {Virus evolution},
volume = {10},
number = {1},
pages = {veae058},
pmid = {39129834},
issn = {2057-1577},
abstract = {Negative sense RNA viruses (NSV) include some of the most detrimental human pathogens, including the influenza, Ebola, and measles viruses. NSV genomes consist of one or multiple single-stranded RNA molecules that are encapsidated into one or more ribonucleoprotein (RNP) complexes. These RNPs consist of viral RNA, a viral RNA polymerase, and many copies of the viral nucleoprotein (NP). Current evolutionary relationships within the NSV phylum are based on the alignment of conserved RNA-dependent RNA polymerase (RdRp) domain amino acid sequences. However, the RdRp domain-based phylogeny does not address whether NP, the other core protein in the NSV genome, evolved along the same trajectory or whether several RdRp-NP pairs evolved through convergent evolution in the segmented and non-segmented NSV genome architectures. Addressing how NP and the RdRp domain evolved may help us better understand NSV diversity. Since NP sequences are too short to infer robust phylogenetic relationships, we here used experimentally obtained and AlphaFold 2.0-predicted NP structures to probe whether evolutionary relationships can be estimated using NSV NP sequences. Following flexible structure alignments of modeled structures, we find that the structural homology of the NSV NPs reveals phylogenetic clusters that are consistent with RdRp-based clustering. In addition, we were able to assign viruses for which RdRp sequences are currently missing to phylogenetic clusters based on the available NP sequence. Both our RdRp-based and NP-based relationships deviate from the current NSV classification of the segmented Naedrevirales, which cluster with the other segmented NSVs in our analysis. Overall, our results suggest that the NSV RdRp and NP genes largely evolved along similar trajectories and even short pieces of genetic, protein-coding information can be used to infer evolutionary relationships, potentially making metagenomic analyses more valuable.},
}
@article {pmid39129757,
year = {2023},
author = {Bloom, JD},
title = {Association between SARS-CoV-2 and metagenomic content of samples from the Huanan Seafood Market.},
journal = {Virus evolution},
volume = {9},
number = {2},
pages = {vead050},
pmid = {39129757},
issn = {2057-1577},
abstract = {The role of the Huanan Seafood Market in the early severe acute respiratory syndrome virus 2 (SARS-CoV-2) outbreak remains unclear. Recently, the Chinese Centers for Disease Control (CDC) released data from deep sequencing of environmental samples collected from the market after it was closed on 1 January 2020. Prior to this release, Crits-Christoph et al. analyzed data from a subset of the samples. Both that study and the Chinese CDC study concurred that the samples contained genetic material from a variety of species, including some like raccoon dogs that are susceptible to SARS-CoV-2. However, neither study systematically analyzed the relationship between the amount of genetic material from SARS-CoV-2 and different animal species. Here I implement a fully reproducible computational pipeline that jointly analyzes the number of reads mapping to SARS-CoV-2 and the mitochondrial genomes of chordate species across the full set of samples. I validate the presence of genetic material from numerous species and calculate mammalian mitochondrial compositions similar to those reported by Crits-Christoph et al. However, the SARS-CoV-2 content of the environmental samples is generally very low: only 21 of 176 samples contain more than ten SARS-CoV-2 reads, despite most samples being sequenced to depths exceeding 10[8] total reads. None of the samples with double-digit numbers of SARS-CoV-2 reads have a substantial fraction of their mitochondrial material from any non-human susceptible species. Only one of the fourteen samples with at least a fifth of the chordate mitochondrial material from raccoon dogs contains any SARS-CoV-2 reads, and that sample only has 1 of ~200,000,000 reads mapping to SARS-CoV-2. Instead, SARS-CoV-2 reads are most correlated with reads mapping to various fish, such as catfish and largemouth bass. These results suggest that while metagenomic analysis of the environmental samples is useful for identifying animals or animal products sold at the market, co-mingling of animal and viral genetic material is unlikely to reliably indicate whether any animals were infected by SARS-CoV-2.},
}
@article {pmid39128916,
year = {2024},
author = {Osburn, ED and McBride, SG and Bahram, M and Strickland, MS},
title = {Global patterns in the growth potential of soil bacterial communities.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {6881},
pmid = {39128916},
issn = {2041-1723},
support = {2020-67034-41310//United States Department of Agriculture | National Institute of Food and Agriculture (NIFA)/ ; 2021-03724//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; 1845417//National Science Foundation (NSF)/ ; },
mesh = {*Soil Microbiology ; *Bacteria/classification/genetics/growth &amp; development/metabolism ; *Soil/chemistry ; *Ecosystem ; *Carbon/metabolism ; Nitrogen/metabolism ; Metagenome ; Forests ; Carbon Cycle ; Microbiota ; Codon Usage ; },
abstract = {Despite the growing catalogue of studies detailing the taxonomic and functional composition of soil bacterial communities, the life history traits of those communities remain largely unknown. This study analyzes a global dataset of soil metagenomes to explore environmental drivers of growth potential, a fundamental aspect of bacterial life history. We find that growth potential, estimated from codon usage statistics, was highest in forested biomes and lowest in arid latitudes. This indicates that bacterial productivity generally reflects ecosystem productivity globally. Accordingly, the strongest environmental predictors of growth potential were productivity indicators, such as distance to the equator, and soil properties that vary along productivity gradients, such as pH and carbon to nitrogen ratios. We also observe that growth potential was negatively correlated with the relative abundances of genes involved in carbohydrate metabolism, demonstrating tradeoffs between growth and resource acquisition in soil bacteria. Overall, we identify macroecological patterns in bacterial growth potential and link growth rates to soil carbon cycling.},
}
@article {pmid39128772,
year = {2024},
author = {Mo, Y and Lim, LS and Ng, SK},
title = {A systematic review on current approaches in bat virus discovered between 2018 and 2022.},
journal = {Journal of virological methods},
volume = {329},
number = {},
pages = {115005},
doi = {10.1016/j.jviromet.2024.115005},
pmid = {39128772},
issn = {1879-0984},
mesh = {*Chiroptera/virology ; Animals ; *Metagenomics/methods ; High-Throughput Nucleotide Sequencing ; Viruses/classification/genetics/isolation &amp; purification ; Genome, Viral ; RNA Viruses/genetics/classification/isolation &amp; purification ; Phylogeny ; DNA Viruses/genetics/classification/isolation &amp; purification ; Virus Diseases/virology/veterinary ; Viral Zoonoses/virology ; },
abstract = {Zoonotic viruses are widely seen as the primary threat for future pandemics. Bats are the most diverse group of mammals, with more than 1400 species distributed across most habitats on Earth. So far, 31 known virus families were associated with bats, although the understanding of most viruses were insufficient. Continuous efforts to discover, understand and monitor these bats viruses, is thereby an area of public health interest. This systematic review was designed to catalogue publications reporting novel bat virus discoveries within PubMed, SCOPUS, and Web of Science databases, within a 5-year period from 2018 to 2022. Various experimental parameters, including sampling locations, methodology, bat species diversity, similarity to known viruses, species demarcation of new viruses, and genomic sequencing strategies, were extracted from 41 publications and analyzed. In total, 72 novel viruses from 19 virus families were identified between 2018 and 2022, particularly from Genomoviridae (DNA viruses) and Coronaviridae (RNA viruses). That said, only a limited number of bat families featured extensively despite noticeable shift towards next generation sequencing methods and metagenomics pipeline for virus identification across different sampling methods. This review aims to provide a comprehensive analysis of the global efforts made over the past five years to identify and characterize emerging viruses in bat species, and to provide a detailed overview of the current technologies and methodologies used in these studies.},
}
@article {pmid39128520,
year = {2024},
author = {Wang, C and Zhu, J and Wang, H and Zhang, L and Li, Y and Zhang, Y and Wu, Z and Zhou, Q},
title = {Sedimentary organic matter load influences the ecological effects of submerged macrophyte restoration through rhizosphere metabolites and microbial communities.},
journal = {The Science of the total environment},
volume = {951},
number = {},
pages = {175419},
doi = {10.1016/j.scitotenv.2024.175419},
pmid = {39128520},
issn = {1879-1026},
mesh = {*Rhizosphere ; *Microbiota ; *Geologic Sediments/microbiology/chemistry ; Lakes ; Phosphorus/metabolism ; Nitrogen/metabolism ; Environmental Restoration and Remediation/methods ; },
abstract = {Organic matter (OM) accumulation in lake sediments has doubled owing to human activities over the past 100 years, which has negatively affected the restoration of submerged vegetation and ecological security. Changes in the pollution structure of sediments caused by plant recovery and rhizosphere chemical processes under different sediment OM levels are the theoretical basis for the rational application of plant rehabilitation technology in lake management. This study explored how Vallisneria natans mediates changes in sediment N and P through rhizospheric metabolites and microbial community and function under low (4.94 %) and high (17.35 %) sediment OM levels. V. natans promoted the accumulation of NH4-N in the high-OM sediment and the transformation of Fe/Al-P to Ca-P in the low-OM sediment. By analyzing 63 rhizospheric metabolites and the sediment microbial metagenome, the metabolites lactic acid and 3-hydroxybutyric acid and the genus Anammoximicrobium were found to mediate NH4-N accumulation in the high-OM sediment. Additionally, 3-hydroxy-decanoic acid, adipic acid, and the genus Bdellovibrionaceae mediated the transformation of Fe/Al-P to Ca-P in the low-OM sediment. The growth of V. natans enriched the abundance of functional genes mediating each step from nitrate to ammonia and the genes encoding urease in the high-OM sediment, and it up-regulated three genes related to microbial phosphorus uptake in the low-OM sediment. This study revealed the necessity of controlling endogenous pollution by recovering submerged macrophytes under high- and low-OM conditions from the perspective of the transformation of inorganic nitrogen and phosphorus.},
}
@article {pmid39128495,
year = {2024},
author = {De Pessemier, B and López, CD and Taelman, S and Verdonck, M and Chen, Y and Stockman, A and Lambert, J and Van de Wiele, T and Callewaert, C},
title = {COMPARATIVE WHOLE METAGENOME ANALYSIS IN LESIONAL AND NON-LESIONAL SCALP AREAS OF PSORIASIS CAPITIS PATIENTS AND HEALTHY INDIVIDUALS.},
journal = {The Journal of investigative dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jid.2024.07.020},
pmid = {39128495},
issn = {1523-1747},
abstract = {Psoriasis is an immune-mediated inflammatory disorder, where the majority of the patients suffer from psoriasis capitis or scalp psoriasis. Current therapeutics remain ineffective to treat scalp lesions. Here, we present a whole-metagenome characterisation of the scalp microbiome in psoriasis capitis. We investigated how changes in the homeostatic cutaneous microbiome correlate with the condition and identified metagenomic biomarkers (taxonomic, functional, virulence factors, antimicrobial resistance genes) that could partly explain its emergence. Within this study, 83 top and back scalp samples from healthy individuals and 64 lesional and non-lesional scalp samples from untreated psoriasis capitis subjects were analysed. Using qPCR targeting the 16S and 18S rRNA genes, we found a significant decrease in microbial load within scalp regions affected by psoriasis compared to their non-lesional counterparts. Metagenomic analysis revealed that psoriatic lesions displayed significant lower Cutibacterium species (incl. C. modestum, C. namnetense, C. granulosum, C. porci), along with an elevation in Staphylococcus aureus. A heightened relative presence of efflux pump protein-encoding genes was detected, suggesting potential antimicrobial resistance mechanisms. These mechanisms are known to specifically target human antimicrobial peptides (incl. cathelicidin LL-37) which are frequently encountered within psoriasis lesions. These shifts in microbial community dynamics may contribute to psoriasis disease pathogenesis.},
}
@article {pmid39127908,
year = {2024},
author = {Jabeen, MF and Sanderson, ND and Tinè, M and Donachie, G and Barber, C and Azim, A and Lau, LCK and Brown, T and Pavord, ID and Chauhan, A and Klenerman, P and Street, TL and Marchi, E and Howarth, PH and Hinks, TSC},
title = {Species-level, metagenomic and proteomic analysis of microbe-immune interactions in severe asthma.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.16269},
pmid = {39127908},
issn = {1398-9995},
support = {//NIHR Primary Care Research Network/ ; //National Institute for Health Research Southampton Biomedical Research Centre/ ; /WT_/Wellcome Trust/United Kingdom ; //NIHR Oxford Biomedical Research Centre/ ; /MRC_/Medical Research Council/United Kingdom ; },
abstract = {BACKGROUND: The airway microbiome in severe asthma has not been characterised at species-level by metagenomic sequencing, nor have the relationships between specific species and mucosal immune responses in 'type-2 low', neutrophilic asthma been defined. We performed an integrated species-level metagenomic data with inflammatory mediators to characterise prevalence of dominant potentially pathogenic organisms and host immune responses.<br><br>METHODS: Sputum and nasal lavage samples were analysed using long-read metagenomic sequencing with Nanopore and qPCR in two cross-sectional adult severe asthma cohorts, Wessex (n&#x2009;=&#x2009;66) and Oxford (n&#x2009;=&#x2009;30). We integrated species-level data with clinical parameters and 39 selected airway proteins measured by immunoassay and O-link.<br><br>RESULTS: The sputum microbiome in health and mild asthma displayed comparable microbial diversity. By contrast, 23% (19/81) of severe asthma microbiomes were dominated by a single respiratory pathogen, namely H. influenzae (n&#x2009;=&#x2009;10), M. catarrhalis (n&#x2009;=&#x2009;4), S. pneumoniae (n&#x2009;=&#x2009;4) and P. aeruginosa (n&#x2009;=&#x2009;1). Neutrophilic asthma was associated with H. influenzae, M. catarrhalis, S. pneumoniae and T. whipplei with elevated type-1 cytokines and proteases; eosinophilic asthma with higher M. catarrhalis, but lower H. influenzae, and S. pneumoniae abundance. H. influenzae load correlated with Eosinophil Cationic Protein, elastase and IL-10. R. mucilaginosa associated positively with IL-6 and negatively with FGF. Bayesian network analysis also revealed close and distinct relationships of H. influenzae and M. catarrhalis with type-1 airway inflammation. The microbiomes and cytokine milieu were distinct between upper and lower airways.<br><br>CONCLUSIONS: This species-level integrated analysis reveals central, but distinct associations between potentially pathogenic bacteria and airways inflammation in severe asthma.},
}
@article {pmid39127849,
year = {2024},
author = {Vigil, BE and Ascue, F and Ayala, RY and Murúa, P and Calderon, MS and Bustamante, DE},
title = {Functional prediction based on 16S rRNA metagenome data from bacterial microbiota associated with macroalgae from the Peruvian coast.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {18577},
pmid = {39127849},
issn = {2045-2322},
support = {Project FitoAlga N&#xb0; PE501079919-2022-PROCIENCIA//Consejo Nacional de Ciencia, Tecnolog&#xed;a e Innovaci&#xf3;n Tecnol&#xf3;gica/ ; },
mesh = {*Seaweed/microbiology ; *RNA, Ribosomal, 16S/genetics ; Peru ; *Metagenome ; *Bacteria/genetics/classification ; *Microbiota/genetics ; Phylogeny ; Biodiversity ; },
abstract = {Macroalgae are vital reservoirs for essential epibiotic microorganisms. Among these are growth-promoting bacteria that support the growth and healthy development of their host macroalgae, and these macroalgae can be utilized in agriculture as biostimulants, offering an alternative to traditional agrochemicals. However, to date, no comparative studies have been conducted on the functional profile and bacterial diversity associated with coastal macroalgae of Peru. In this study, we employed amplicon sequencing of the V3-V4 region of 16S rRNA gene in twelve host macroalgae collected from two rocky shores in central Peru to compare their bacterial communities. The results revealed high bacterial diversity across both sites, but differences in microbial composition were noted. The phyla Bacteroidota and Pseudomonadota were predominant. The functional prediction highlighted 44 significant metabolic pathways associated with the bacterial microbiota when comparing host macroalgae. These active pathways are related to metabolism and genetic and cellular information processing. No direct association was detected between the macroalgal genera and the associated microbiota, suggesting that the bacterial community is largely influenced by their genetic functions than the taxonomic composition of their hosts. Furthermore, some species of Chlorophyta and Rhodophyta were observed to host growth-promoting bacteria, such as Maribacter sp. and Sulfitobacter sp.},
}
@article {pmid39127718,
year = {2024},
author = {Van Uffelen, A and Posadas, A and Roosens, NHC and Marchal, K and De Keersmaecker, SCJ and Vanneste, K},
title = {Benchmarking bacterial taxonomic classification using nanopore metagenomics data of several mock communities.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {864},
pmid = {39127718},
issn = {2052-4463},
mesh = {*Metagenomics/methods ; *Benchmarking ; *Bacteria/genetics/classification ; Nanopore Sequencing ; Nanopores ; Microbiota ; },
abstract = {Taxonomic classification is crucial in identifying organisms within diverse microbial communities when using metagenomics shotgun sequencing. While second-generation Illumina sequencing still dominates, third-generation nanopore sequencing promises improved classification through longer reads. However, extensive benchmarking studies on nanopore data are lacking. We systematically evaluated performance of bacterial taxonomic classification for metagenomics nanopore sequencing data for several commonly used classifiers, using standardized reference sequence databases, on the largest collection of publicly available data for defined mock communities thus far (nine samples), representing different research domains and application scopes. Our results categorize classifiers into three categories: low precision/high recall; medium precision/medium recall, and high precision/medium recall. Most fall into the first group, although precision can be improved without excessively penalizing recall with suitable abundance filtering. No definitive 'best' classifier emerges, and classifier selection depends on application scope and practical requirements. Although few classifiers designed for long reads exist, they generally exhibit better performance. Our comprehensive benchmarking provides concrete recommendations, supported by publicly available code for reassessment and fine-tuning by other scientists.},
}
@article {pmid39127363,
year = {2024},
author = {Yun, Y and Lv, T and Gui, Z and Su, T and Cao, W and Tian, X and Chen, Y and Wang, S and Jia, Z and Li, G and Ma, T},
title = {Composition and metabolic flexibility of hydrocarbon-degrading consortia in oil reservoirs.},
journal = {Bioresource technology},
volume = {409},
number = {},
pages = {131244},
doi = {10.1016/j.biortech.2024.131244},
pmid = {39127363},
issn = {1873-2976},
mesh = {*Hydrocarbons/metabolism ; *Biodegradation, Environmental ; *Oil and Gas Fields/microbiology ; Microbial Consortia/physiology ; Bacteria/metabolism ; Petroleum/metabolism ; Phylogeny ; },
abstract = {Hydrocarbon-degrading consortia (HDC) play an important role in petroleum exploitation. However, the real composition and metabolic mechanism of HDC in the microbial enhanced oil recovery (MEOR) process remain unclear. By combining [13]C-DNA stable isotope probing microcosms with metagenomics, some newly reported phyla, including Chloroflexi, Synergistetes, Thermotogae, and Planctomycetes, dominated the HDC in the oil reservoirs. In the field trials, the HDC in the aerobic-facultative-anaerobic stage of oilfields jointly promoted the MEOR process, with monthly oil increments of up to 189 tons. Pseudomonas can improve oil recovery by producing rhamnolipid in the facultative condition. Roseovarius was the novel taxa potentially oxidizing alkane and producing acetate to improve oil porosity and permeability in the aerobic condition. Ca. Bacteroidia were the new members potentially degrading hydrocarbons by fumarate addition in the anaerobic environment. Comprehensive identification of the active HDC in oil reservoirs provides a novel theoretical basis for oilfield regulatory scheme.},
}
@article {pmid39127355,
year = {2024},
author = {Wang, P and Tan, J and Xiao, Z and Xu, F and Jin, Q and He, D},
title = {New insights and enhancement mechanisms of activated carbon in autotrophic denitrification system utilizing zero-valent iron as indirect electron donors.},
journal = {Bioresource technology},
volume = {410},
number = {},
pages = {131237},
doi = {10.1016/j.biortech.2024.131237},
pmid = {39127355},
issn = {1873-2976},
mesh = {*Denitrification ; *Iron/metabolism ; *Autotrophic Processes ; *Electrons ; *Nitrogen/metabolism ; Charcoal/chemistry ; Oxidation-Reduction ; Sewage/microbiology ; Bacteria/metabolism ; Bioreactors ; Nitrates/metabolism ; },
abstract = {Zero-valent iron acts as an indirect electron donor, supplying ferrous iron for the nitrate-dependent ferrous oxidation (NDFO) process. The addition of activated carbon (AC) increased the specific NDFO activity in situ and ex situ by 0.4 mg-N/(d·g VSS) and 2.2 mg-N/(d·g VSS), respectively, due to the enrichment of NDFO bacteria. Furthermore, AC reduced the nitrous oxide emission potential of the sludge, a mechanism that metagenomic analysis suggests may act as a cellular energy storage strategy. During a 196-day experiment, a total nitrogen removal efficiency of 53.7 % was achieved, which may be attributed to the upregulation of key genes involved in iron oxidation and denitrification. Based on these findings, a model involving pilin, 'nanowires,' and a cyc2/?→/(FoxE→FoxY)/?→cymA/Complex III/?-mediated pathway for extracellular electron uptake was proposed. Overall, this work provides a feasible strategy for enhancing the nitrogen removal performance of the ZVI-NDFO process.},
}
@article {pmid39127317,
year = {2024},
author = {Tang, W and Wang, Q and Sun, M and Liu, C and Huang, Y and Zhou, M and Zhang, X and Meng, Z and Zhang, J},
title = {The gut microbiota-oligodendrocyte axis: A promising pathway for modulating oligodendrocyte homeostasis and demyelination-associated disorders.},
journal = {Life sciences},
volume = {354},
number = {},
pages = {122952},
doi = {10.1016/j.lfs.2024.122952},
pmid = {39127317},
issn = {1879-0631},
mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; Animals ; *Oligodendroglia/metabolism ; *Homeostasis/physiology ; *Demyelinating Diseases/metabolism/microbiology ; *Brain-Gut Axis/physiology ; Dysbiosis/microbiology ; Myelin Sheath/metabolism ; },
abstract = {The bidirectional regulation between the gut microbiota and brain, known as gut-brain axis, has received significant attention. The myelin sheath, produced by oligodendrocytes or Schwann cells, is essential for efficient nervous signal transmission and the maintenance of brain function. Growing evidence shows that both oligodendrogenesis and myelination are modulated by gut microbiota and its metabolites, and when dysbiosis occurs, changes in the microbiota composition and/or associated metabolites may impact developmental myelination and the occurrence of neurodevelopmental disabilities. Although the link between the microbiota and demyelinating disease such as multiple sclerosis has been extensively studied, our knowledge about the role of the microbiota in other myelin-related disorders, such as neurodegenerative diseases, is limited. Mechanistically, the microbiota-oligodendrocyte axis is primarily mediated by factors such as inflammation, the vagus nerve, endocrine hormones, and microbiota metabolites as evidenced by metagenomics, metabolomics, vagotomy, and morphological and molecular approaches. Treatments targeting this axis include probiotics, prebiotics, microbial metabolites, herbal bioactive compounds, and specific dietary management. In addition to the commonly used approaches, viral vector-mediated tracing and gene manipulation, integrated multiomics and multicenter clinical trials will greatly promote the mechanistic and interventional studies and ultimately, the development of new preventive and therapeutic strategies against gut-oligodendrocyte axis-mediated brain impairments. Interestingly, recent findings showed that microbiota dysbiosis can be induced by hippocampal myelin damage and is reversible by myelin-targeted drugs, which provides new insights into understanding how hippocampus-based functional impairment (such as in neurodegenerative Alzheimer's disease) regulates the peripheral homeostasis of microbiota and associated systemic disorders.},
}
@article {pmid39127210,
year = {2024},
author = {Liu, R and Chang, D and Zhou, G and Liang, H and Zhang, J and Chai, Q and Cao, W},
title = {Green manuring combined with zeolite reduced nitrous oxide emissions in maize field by targeting microbial nitrogen transformations.},
journal = {The Science of the total environment},
volume = {950},
number = {},
pages = {175382},
doi = {10.1016/j.scitotenv.2024.175382},
pmid = {39127210},
issn = {1879-1026},
mesh = {*Zeolites ; *Nitrous Oxide/analysis ; *Zea mays ; *Manure ; *Nitrogen/analysis ; Air Pollutants/analysis ; Agriculture/methods ; Fertilizers/analysis ; Soil Microbiology ; },
abstract = {Green manure is a crucial strategy for increasing cereal yield and mitigating environmental burden while reducing chemical N fertilizer. To effectively tackle climate change, finding ways to reduce nitrous oxide (N2O) emissions from green manuring systems is vital. Herein, field and [15]N labeled microcosm experiments were arranged to investigate the effect and mechanisms of green manuring and zeolite application on N2O emission. Both experiments comprised four treatments: conventional chemical N (N100), 70 % chemical N (N70), N70 with green manure (N70 + CV), and N70 + CV combined with zeolite (N70 + CV + Z). Compared with N100, both N70 + CV and N70 + CV + Z maintained maize yield, cumulative N2O emissions decreased by 37.7 % and 34.9 % in N70 + CV + Z in 2022-yr and 2023-yr, and by 12.8 % in N70 + CV in 2022-yr. Moreover, the reduction of N2O emission primarily occurred after incorporating green manure. The N100 and N70 + CV demonstrated a similar transformed proportion of chemical N to N2O (i.e., 4.9 % and 4.7 %) while reducing it to 2.7 % in N70 + CV + Z. Additionally, a mere 0.7 % of green manure N was transformed to N2O in both N70 + CV and N70 + CV + Z treatments. Compared with N100, both N70 + CV and N70 + CV + Z decreased the relative abundances of ammonia oxidation microbes, increased denitrifier and the ratios of (nirK + nirS)/nosZ and norBC/nosZ. Furthermore, compared with N70 + CV, N70 + CV + Z decreased the relative abundances of N2O-producer and the ratios of (nirK + nirS)/nosZ and norBC/nosZ in denitrification. These findings revealed that the reduction of N2O emissions resulting from green manure replaced chemical N was mainly due to weakened nitrification, while zeolite reduced N2O emissions attributed to enhanced conversion of N2O to N2. Moreover, certain key N-cycling functional bacteria, such as Phycisphaerae, Rubrobacteria, and Thermoflexia, were positively correlated with N2O emission. In contrast, Dehalococcoidia, Gammaproteobacteria, and Betaproteobacteria were negatively correlated with N2O emission. This investigation uncovered the underlying mechanisms for effectively reducing N2O emissions through green manuring combined with zeolite.},
}
@article {pmid39126385,
year = {2024},
author = {Jangi, S and Zhao, N and Hsia, K and Park, YS and Michaud, DS and Yoon, H},
title = {Specific bacterial co-abundance groups are associated with inflammatory status in patients with ulcerative colitis.},
journal = {Journal of Crohn's &amp; colitis},
volume = {},
number = {},
pages = {},
doi = {10.1093/ecco-jcc/jjae125},
pmid = {39126385},
issn = {1876-4479},
abstract = {BACKGROUND AND AIMS: While there is increasing interest in microbiome-directed therapies for patients with ulcerative colitis (UC), the identification of microbial targets remains elusive, underlining the need for novel approaches.<br><br>METHODS: Utilizing metagenomic data from the Study of a Prospective Adult Research Cohort with Inflammatory Bowel Disease, available via the IBD Plexus Program of the Crohn's &amp; Colitis Foundation, we used a tree-based dichotomous approach to assemble distinct clusters of species-level bacterial co-abundance groups (CAGs). We evaluated the abundance of bacterial CAGs and fungal taxa during remission (n=166) and activity (n=46). We examined if the bacterial CAGs identified in our cohorts were conserved in 2 healthy cohorts and in a Korean UC cohort.<br><br>RESULTS: CAG3 and CAG8, dominated by bacteria from family Lachnospiraceae, were associated with remission. Low CAG8 and elevated Candida genus were predictive of active UC. Constituents from CAG8 were influential hub species of the remission-associated microbial UC network, including Ruminococcus gnavus, Erysipelatoclostridium ramosum, Blautia and Dorea species. These hub species interactions were preserved in 2 healthy cohorts and were partially recapitulated in a Korean UC cohort. CAG8 abundance correlated with the secondary bile acid production pathway. Bacterial CAGs did not correlate with Candida, however Bifidobacterium adolescentis and Alistipes putredinis were negatively associated with Candida.<br><br>CONCLUSIONS: Lachnospiriceae-dominated bacterial CAGs were associated with remission in UC, with key bacterial interactions within the CAG also observed in 2 healthy cohorts and a Korean UC cohort. Bacterial CAG-based analyses may help to inform the design of candidate consortia for microbiome-based therapeutics.},
}
@article {pmid39125688,
year = {2024},
author = {Ercolano, C and Iacono, R and Cafaro, V and Pizzo, E and Giovannelli, D and Feuerriegel, G and Streit, WR and Strazzulli, A and Moracci, M},
title = {Biochemical Characterisation of Sis: A Distinct Thermophilic PETase with Enhanced NanoPET Substrate Hydrolysis and Thermal Stability.},
journal = {International journal of molecular sciences},
volume = {25},
number = {15},
pages = {},
pmid = {39125688},
issn = {1422-0067},
support = {2020SBNHLH_003//Ministero dell'Universit&#xe0; e della Ricerca (MUR)/ ; },
mesh = {*Polyethylene Terephthalates/chemistry/metabolism ; Hydrolysis ; *Enzyme Stability ; Phylogeny ; Temperature ; Substrate Specificity ; Kinetics ; Hydrolases/chemistry/metabolism ; Bacterial Proteins/chemistry/metabolism/genetics ; },
abstract = {Polyethylene terephthalate (PET) degradation by enzymatic hydrolysis is significant for addressing plastic pollution and fostering sustainable waste management practices. Identifying thermophilic and thermostable PET hydrolases is particularly crucial for industrial bioprocesses, where elevated temperatures may enhance enzymatic efficiency and process kinetics. In this study, we present the discovery of a novel thermophilic and thermostable PETase enzyme named Sis, obtained through metagenomic sequence-based analysis. Sis exhibits robust activity on nanoPET substrates, demonstrating effectiveness at temperatures up to 70 °C and displaying exceptional thermal stability with a melting temperature (Tm) of 82 °C. Phylogenetically distinct from previously characterised PET hydrolases, Sis represents a valuable addition to the repertoire of enzymes suitable for PET degradation.},
}
@article {pmid39125621,
year = {2024},
author = {Jelin-Uhlig, S and Weigel, M and Ott, B and Imirzalioglu, C and Howaldt, HP and Böttger, S and Hain, T},
title = {Bisphosphonate-Related Osteonecrosis of the Jaw and Oral Microbiome: Clinical Risk Factors, Pathophysiology and Treatment Options.},
journal = {International journal of molecular sciences},
volume = {25},
number = {15},
pages = {},
pmid = {39125621},
issn = {1422-0067},
support = {DZIF-MD / 80325MD058//German Center for Infection Research/ ; },
mesh = {Humans ; *Bisphosphonate-Associated Osteonecrosis of the Jaw/etiology/microbiology ; *Microbiota/drug effects ; Risk Factors ; *Diphosphonates/adverse effects/therapeutic use ; Mouth/microbiology ; },
abstract = {Bisphosphonate-related osteonecrosis of the jaw (BRONJ) represents a serious health condition, impacting the lives of many patients worldwide. The condition challenges clinical care due to its complex etiology and limited therapeutic options. A thorough understanding of the pathophysiological and patient-related factors that promote disease development is essential. Recently, the oral microbiome has been implicated as a potential driver and modulating factor of BRONJ by several studies. Modern genomic sequencing methods have provided a wealth of data on the microbial composition of BRONJ lesions; however, the role of individual species in the process of disease development remains elusive. A comprehensive PubMed search was conducted to identify relevant studies on the microbiome of BRONJ patients using the terms "microbiome", "osteonecrosis of the jaws", and "bisphosphonates". Studies focusing on symptoms, epidemiology, pathophysiology, risk factors, and treatment options were included. The principal risk factors for BRONJ are tooth extraction, surgical procedures, and the administration of high doses of bisphosphonates. Importantly, the oral microbiome plays a significant role in the progression of the disease. Several studies have identified alterations of microbial composition in BRONJ lesions. However, there is no consensus regarding bacterial species that are associated with BRONJ across studies. The bacterial genera typically found include Actinomyces, Fusobacterium, and Streptococcus. It is postulated that these microbes contribute to the pathogenesis of BRONJ by promoting inflammation and disrupting normal bone remodeling processes. Current therapeutic approaches are disease-stage-specific and the necessity for more effective treatment strategies remains. This review examines the potential causes of and therapeutic approaches to BRONJ, highlighting the link between microbial colonization and BRONJ development. Future research should seek to more thoroughly investigate the interactions between bisphosphonates, the oral microbiome, and the immune system in order to develop targeted therapies.},
}
@article {pmid39125593,
year = {2024},
author = {Kulecka, M and Czarnowski, P and Bałabas, A and Turkot, M and Kruczkowska-Tarantowicz, K and Żeber-Lubecka, N and Dąbrowska, M and Paszkiewicz-Kozik, E and Walewski, J and Ługowska, I and Koseła-Paterczyk, H and Rutkowski, P and Kluska, A and Piątkowska, M and Jagiełło-Gruszfeld, A and Tenderenda, M and Gawiński, C and Wyrwicz, L and Borucka, M and Krzakowski, M and Zając, L and Kamiński, M and Mikula, M and Ostrowski, J},
title = {Microbial and Metabolic Gut Profiling across Seven Malignancies Identifies Fecal Faecalibacillus intestinalis and Formic Acid as Commonly Altered in Cancer Patients.},
journal = {International journal of molecular sciences},
volume = {25},
number = {15},
pages = {},
pmid = {39125593},
issn = {1422-0067},
support = {2017/27/B/NZ5/01504//National Science Center/ ; 2018/31/B/NZ7/02675//National Science Center/ ; 2020/ABM/01/00004//The Medical Research Agency/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Female ; *Feces/microbiology ; Male ; *Formates/metabolism ; Middle Aged ; Aged ; Neoplasms/metabolism/microbiology ; Adult ; Dysbiosis/microbiology ; Metabolomics/methods ; Metabolome ; Gas Chromatography-Mass Spectrometry ; Metagenomics/methods ; },
abstract = {The key association between gut dysbiosis and cancer is already known. Here, we used whole-genome shotgun sequencing (WGS) and gas chromatography/mass spectrometry (GC/MS) to conduct metagenomic and metabolomic analyses to identify common and distinct taxonomic configurations among 40, 45, 71, 34, 50, 60, and 40 patients with colorectal cancer, stomach cancer, breast cancer, lung cancer, melanoma, lymphoid neoplasms and acute myeloid leukemia (AML), respectively, and compared the data with those from sex- and age-matched healthy controls (HC). α-diversity differed only between the lymphoid neoplasm and AML groups and their respective HC, while β-diversity differed between all groups and their HC. Of 203 unique species, 179 and 24 were under- and over-represented, respectively, in the case groups compared with HC. Of these, Faecalibacillus intestinalis was under-represented in each of the seven groups studied, Anaerostipes hadrus was under-represented in all but the stomach cancer group, and 22 species were under-represented in the remaining five case groups. There was a marked reduction in the gut microbiome cancer index in all case groups except the AML group. Of the short-chain fatty acids and amino acids tested, the relative concentration of formic acid was significantly higher in each of the case groups than in HC, and the abundance of seven species of Faecalibacterium correlated negatively with most amino acids and formic acid, and positively with the levels of acetic, propanoic, and butanoic acid. We found more differences than similarities between the studied malignancy groups, with large variations in diversity, taxonomic/metabolomic profiles, and functional assignments. While the results obtained may demonstrate trends rather than objective differences that correlate with different types of malignancy, the newly developed gut microbiota cancer index did distinguish most of the cancer cases from HC. We believe that these data are a promising step forward in the search for new diagnostic and predictive tests to assess intestinal dysbiosis among cancer patients.},
}
@article {pmid39125549,
year = {2024},
author = {Brożek-Mądry, E and Burska, Z and Życińska, K and Sierdziński, J},
title = {Nasal Microbiome in Granulomatosis with Polyangiitis Compared to Chronic Rhinosinusitis.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {14},
number = {15},
pages = {},
pmid = {39125549},
issn = {2075-4418},
abstract = {Rhinosinusitis in granulomatosis with polyangiitis (GPA) is categorised as a secondary, diffuse and inflammatory chronic rhinosinusitis (CRS). It is one of the conditions that impacts the nasal microbiota. This study aimed to compare the nasal microbiomes of patients with GPA, CRS and NSP. A total of 31 patients were included in the study (18 GPA, 6 CRS and 7 nasal septum perforation (NSP)). In all patients, SNOT 22, a nasal endoscopy (Lund-Kennedy scale) and a brush swab were performed. The metagenomic analysis was carried out based on the hypervariable V3-V4 region of the 16S rRNA gene. At the genus level, statistically significant differences were observed in two comparisons: the GPA/NSP and the GPA/CRS groups. In the GPA/NSP group, the differences were related to four genera (Actinomyces, Streptococcus, Methylobacterium-Methylorubrum, Paracoccus), while in the GPA/CRS group, they were related to six (Kocuria, Rothia, Cutibacterium, Streptococcus, Methylobacterium-Methylorubrum, Tepidimonas). Patients with GPA had lower diversity compared to CRS and NSP patients. There were no statistically significant differences found for the Staphylococcus family and Staphylococcus aureus between the three groups.},
}
@article {pmid39125474,
year = {2024},
author = {Mirabile, A and Sangiorgio, G and Bonacci, PG and Bivona, D and Nicitra, E and Bonomo, C and Bongiorno, D and Stefani, S and Musso, N},
title = {Advancing Pathogen Identification: The Role of Digital PCR in Enhancing Diagnostic Power in Different Settings.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {14},
number = {15},
pages = {},
pmid = {39125474},
issn = {2075-4418},
support = {PE 00000007 INF-ACT//Ministry of Education, Universities and Research/ ; SAMOTHRACE ECS00000022//Ministry of Education, Universities and Research/ ; },
abstract = {Digital polymerase chain reaction (dPCR) has emerged as a groundbreaking technology in molecular biology and diagnostics, offering exceptional precision and sensitivity in nucleic acid detection and quantification. This review highlights the core principles and transformative potential of dPCR, particularly in infectious disease diagnostics and environmental surveillance. Emphasizing its evolution from traditional PCR, dPCR provides accurate absolute quantification of target nucleic acids through advanced partitioning techniques. The review addresses the significant impact of dPCR in sepsis diagnosis and management, showcasing its superior sensitivity and specificity in early pathogen detection and identification of drug-resistant genes. Despite its advantages, challenges such as optimization of experimental conditions, standardization of data analysis workflows, and high costs are discussed. Furthermore, we compare various commercially available dPCR platforms, detailing their features and applications in clinical and research settings. Additionally, the review explores dPCR's role in water microbiology, particularly in wastewater surveillance and monitoring of waterborne pathogens, underscoring its importance in public health protection. In conclusion, future prospects of dPCR, including methodological optimization, integration with innovative technologies, and expansion into new sectors like metagenomics, are explored.},
}
@article {pmid39123781,
year = {2024},
author = {Wang, H and Zhan, J and Jiang, H and Jia, H and Pan, Y and Zhong, X and Huo, J and Zhao, S},
title = {Metagenomics-Metabolomics Exploration of Three-Way-Crossbreeding Effects on Rumen to Provide Basis for Crossbreeding Improvement of Sheep Microbiome and Metabolome of Sheep.},
journal = {Animals : an open access journal from MDPI},
volume = {14},
number = {15},
pages = {},
pmid = {39123781},
issn = {2076-2615},
support = {JXSNKYJCRC202407, JXSNKYJCRC202445//Basic Research and Talent Training, Jiangxi Academy of Agricultural Sciences/ ; JXARS-13//Earmarked Fund for Jiangxi Agriculture Research System/ ; },
abstract = {The objective of this experiment was to explore the effects of three-way hybridization on rumen microbes and metabolites in sheep using rumen metagenomics and metabolomics. Healthy Hu and CAH (Charolais × Australian White × Hu) male lambs of similar birth weight and age were selected for short-term fattening after intensive weaning to collect rumen fluid for sequencing. Rumen metagenomics diversity showed that Hu and CAH sheep were significantly segregated at the species, KEGG-enzyme, and CAZy-family levels. Moreover, the CAH significantly increased the ACE and Chao1 indices. Further, correlation analysis of the abundance of the top 80 revealed that the microorganisms were interrelated at the species, KEGG-enzyme, and CAZy-family levels. Overall, the microbiome significantly affected metabolites of the top five pathways, with the strongest correlation found with succinic acid. Meanwhile, species-level microbial markers significantly affected rumen differential metabolites. In addition, rumen microbial markers in Hu sheep were overall positively correlated with down-regulated metabolites and negatively correlated with up-regulated metabolites. In contrast, rumen microbial markers in CAH lambs were overall negatively correlated with down-regulated metabolites and positively correlated with up-regulated metabolites. These results suggest that three-way crossbreeding significantly affects rumen microbial community and metabolite composition, and that significant interactions exist between rumen microbes and metabolites.},
}
@article {pmid39123724,
year = {2024},
author = {Wei, P and Sun, W and Hao, S and Deng, L and Zou, W and Wu, H and Lu, W and He, Y},
title = {Dietary Supplementation of Crossbred Pigs with Glycerol, Vitamin C, and Niacinamide Alters the Composition of Gut Flora and Gut Flora-Derived Metabolites.},
journal = {Animals : an open access journal from MDPI},
volume = {14},
number = {15},
pages = {},
pmid = {39123724},
issn = {2076-2615},
support = {JXXTCX2016003-02//Jiangxi Modern Agricultural Research Collaborative Innovation Project/ ; },
abstract = {The addition of glycerin, vitamin C, and niacinamide to pig diets increased the redness of longissimus dorsi; however, it remains unclear how these supplements affect gut microbiota and metabolites. A total of 84 piglets (20.35 ± 2.14 kg) were randomly allotted to groups A (control), B (glycerin-supplemented), C (vitamin C and niacinamide-supplemented), and D (glycerin, vitamin C and niacinamide-supplemented) during a feeding experiment. Metagenomic and metabolomic technologies were used to analyze the fecal compositions of bile acids, metabolites, and microbiota. The results showed that compared to pigs in group A, pigs in group D had lower virulence factor expressions of lipopolysaccharide (p < 0.05), fatty acid resistance system (p < 0.05), and capsule (p < 0.01); higher fecal levels of ferric ion (p < 0.05), allolithocholic acid (p < 0.01), deoxycholic acid (p < 0.05), tauroursodeoxycholic acid dihydrate (p < 0.01), glycodeoxycholic acid (p < 0.05), L-proline (p < 0.01) and calcitriol (p < 0.01); and higher (p < 0.05) abundances of iron-acquiring microbiota (Methanobrevibacter, Clostridium, Clostridiaceae, Clostridium_sp_CAG_1000, Faecalibacterium_sp_CAG_74_58_120, Eubacteriales_Family_XIII_Incertae_Sedis, Alistipes_sp_CAG_435, Alistipes_sp_CAG_514 and Methanobrevibacter_sp_YE315). Supplementation with glycerin, vitamin C, and niacinamide to pigs significantly promoted the growth of iron-acquiring microbiota in feces, reduced the expression of some virulence factor genes of fecal pathogens, and increased the fecal levels of ferric ion, L-proline, and some secondary bile acids. The administration of glycerol, vitamin C, and niacinamide to pigs may serve as an effective measure for muscle redness improvement by altering the compositions of fecal microbiota and metabolites.},
}
@article {pmid39123642,
year = {2024},
author = {Yan, Y and Liang, Z and Huo, Y and Wu, Q and Ni, L and Lv, X},
title = {A Comparative Study of Microbial Communities, Biogenic Amines, and Volatile Profiles in the Brewing Process of Rice Wines with Hongqu and Xiaoqu as Fermentation Starters.},
journal = {Foods (Basel, Switzerland)},
volume = {13},
number = {15},
pages = {},
pmid = {39123642},
issn = {2304-8158},
support = {No. 2022J01101//Natural Science Foundation of Fujian Province of China/ ; No. 32072204//National Natural Science Foundation of China/ ; No. 2022L3075//Central Leading Local Science and Technology Development Fund Project of China/ ; },
abstract = {Rice wine is primarily crafted from grains through saccharification and liquification with the help of Qu. Qu plays an important role in the formation of the flavor quality of rice wine. Hongqu and Xiaoqu represent two prevalent varieties of Qu that are typically utilized in the brewing process of rice wine and play a crucial role in its production. In this study, GC, GC-MS, HPLC, and metagenomic sequencing techniques were used to contrast the microbial flora, biogenic amines, and aroma characteristics developed during the fermentation of rice wines, with Hongqu and Xiaoqu being used as initiating agents for the brewing process. The results show that the content of higher alcohols (including n-propanol, isobutanol, 3-methyl-1-butanol, and phenethyl alcohol) in rice wine brewed with Xiaoqu (XQW) was significantly higher than that in rice wine brewed with Hongqu (HQW). Contrarily, the concentration of biogenic amines in HQW surpassed that of XQW by a notable margin, but tyramine was significantly enriched in XQW and not detected in HQW. In addition, a multivariate statistical analysis revealed distinct disparities in the constitution of volatile components between HQW and XQW. Hexanoic acid, ethyl acetate, isoamyl acetate, ethyl caproate, ethyl decanoate, 2-methoxy-4-vinylphenol, etc., were identified as the characteristic aroma-active compounds in HQW and XQW. A microbiome analysis based on metagenomic sequencing showed that HQW and XQW had different dominant microorganisms in the brewing process. Burkholderia, Klebsiella, Leuconostoc, Monascus, and Aspergillus were identified as the primary microbial genera in the HQW fermentation period, while Pediococcus, Enterobacter, Rhizopus, Ascoidea, and Wickerhamomyces were the main microbial genera in the XQW brewing process. A bioinformatics analysis revealed that the concentrations of microbial genes involved in biogenic amines and esters biosynthesis were significantly higher in HQW than those in XQW, while the content of genes relevant to glycolysis, higher alcohol biosynthesis, and fatty acid metabolism was significantly higher in XQW than in HQW, which are the possible reasons for the difference in flavor quality between the two kinds of rice wine from the perspective of microbial functional genes.},
}
@article {pmid39123524,
year = {2024},
author = {Todhanakasem, T and Van Tai, N and Pornpukdeewattana, S and Charoenrat, T and Young, BM and Wattanachaisaereekul, S},
title = {The Relationship between Microbial Communities in Coffee Fermentation and Aroma with Metabolite Attributes of Finished Products.},
journal = {Foods (Basel, Switzerland)},
volume = {13},
number = {15},
pages = {},
pmid = {39123524},
issn = {2304-8158},
support = {RE-KRIS/FF66/66//Fundamental fund/ ; },
abstract = {Coffee is a critical agricultural commodity and is used to produce premium beverages enjoyed by people worldwide. The microbiome of coffee beans has proven to be an essential tool that improves the flavor profile of coffee by creating aromatic flavor compounds through natural fermentation. This study investigated the natural microbial consortium during the wet process fermentation of coffee onsite in Thailand in order to identify the correlation between microbial diversity and biochemical characteristics including flavor, aroma, and metabolic attributes. Our study found 64 genera of bacteria and 59 genera of yeast/fungi present during the fermentation process. Group of microbes, mainly yeast and lactic acid bacteria, that predominated in the process were significantly correlated with preferable flavor and aroma compounds, including linalyl formate, linalool, cis-isoeugenol, trans-geraniol, and (-)-isopulegol. Some of the detected metabolites were found to be active compounds which could play a role in health.},
}
@article {pmid39123456,
year = {2024},
author = {Kafida, M and Karela, M and Giakountis, A},
title = {RNA-Independent Regulatory Functions of lncRNA in Complex Disease.},
journal = {Cancers},
volume = {16},
number = {15},
pages = {},
pmid = {39123456},
issn = {2072-6694},
abstract = {During the metagenomics era, high-throughput sequencing efforts both in mice and humans indicate that non-coding RNAs (ncRNAs) constitute a significant fraction of the transcribed genome. During the past decades, the regulatory role of these non-coding transcripts along with their interactions with other molecules have been extensively characterized. However, the study of long non-coding RNAs (lncRNAs), an ncRNA regulatory class with transcript lengths that exceed 200 nucleotides, revealed that certain non-coding transcripts are transcriptional "by-products", while their loci exert their downstream regulatory functions through RNA-independent mechanisms. Such mechanisms include, but are not limited to, chromatin interactions and complex promoter-enhancer competition schemes that involve the underlying ncRNA locus with or without its nascent transcription, mediating significant or even exclusive roles in the regulation of downstream target genes in mammals. Interestingly, such RNA-independent mechanisms often drive pathological manifestations, including oncogenesis. In this review, we summarize selective examples of lncRNAs that regulate target genes independently of their produced transcripts.},
}
@article {pmid39123272,
year = {2024},
author = {Gong, X and Xu, L and Langwig, MV and Chen, Z and Huang, S and Zhao, D and Su, L and Zhang, Y and Francis, CA and Liu, J and Li, J and Baker, BJ},
title = {Globally distributed marine Gemmatimonadota have unique genomic potentials.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {149},
pmid = {39123272},
issn = {2049-2618},
support = {2020YFA0608301//National Key Research and Development Program of China/ ; 92351302//National Natural Science Foundation of China/ ; 42072333//National Natural Science Foundation of China/ ; MGK202009//State Key Laboratory of Marine Geology, Tongji University/ ; 2021HJ01//PI Project of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; LI-SIAME-00002001//Simons Foundation/ ; },
mesh = {*Phylogeny ; *Metagenome ; Genome, Bacterial ; Geologic Sediments/microbiology ; Genomics ; Seawater/microbiology ; Aquatic Organisms/genetics ; Secondary Metabolism ; Metagenomics ; },
abstract = {BACKGROUND: Gemmatimonadota bacteria are widely distributed in nature, but their metabolic potential and ecological roles in marine environments are poorly understood.<br><br>RESULTS: Here, we obtained 495 metagenome-assembled genomes (MAGs), and associated viruses, from coastal to deep-sea sediments around the world. We used this expanded genomic catalog to compare the protein composition and update the phylogeny of these bacteria. The marine Gemmatimonadota are phylogenetically different from those previously reported from terrestrial environments. Functional analyses of these genomes revealed these marine genotypes are capable of degradation of complex organic carbon, denitrification, sulfate reduction, and oxidizing sulfide and sulfite. Interestingly, there is widespread genetic potential for secondary metabolite biosynthesis across Gemmatimonadota, which may represent an unexplored source of novel natural products. Furthermore, viruses associated with Gemmatimonadota have the potential to "hijack" and manipulate host metabolism, including the assembly of the lipopolysaccharide in their hosts.<br><br>CONCLUSIONS: This expanded genomic diversity advances our understanding of these globally distributed bacteria across a variety of ecosystems and reveals genetic distinctions between those in terrestrial and marine communities. Video Abstract.},
}
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